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Have you got a link to the site Matthew? I'll take a look.
It sounds like just a replication of the menu to me? If so, this is perfectly fine - it just means more links going to the pages. If both links point to the exact same URL's then there are no issues at all.
It can be a pretty big job if you change the URL structures - depending on how large the website is.
Modesto Siotos wrote a blog on it here.
If you change the structure then ideally, you should forward every page to the closest replacement page on the new design using a 301.
Give the blog a good read, it should hopefully help.
Matt
I have taken this from a similar question I answered not long ago...
"I will try and keep this as basic as possible so if you need me to elaborate, please ask.
The best way to start (and often a step that people forget completely) is to approach company's who you already have had dealings with. Try some of the following:
Accountants, Solicitors, Suppliers, Friends, Local Newspapers, Customers, Marketing Company's, Software Company's... Any business that you have dealt with. It could be a plumber who fitted the kitchen, the builder who built the building, a welder who made your gate... Anything!
Chances are, these websites wont be that relevant to your market (and maybe not even very good) but they are always an important place to start.
Be creativewhen approaching them though - chances are they won't just want to link to you for no reason. Maybe write them an article for their blog or news section on their website. Maybe write a testimonial saying how pleased you are with them or their service and link back to your site within the testimonial.
Next on the list is to ask your website designer for a link (if you have one). If he/she is proud of the work they carried out, they would happily add your website to their portfolio on their own website and link to your site.
If you had a logo designed and think it looks pretty sexy, show it off! There are lots of logo directories that will have your logo on their site with a link back to your site.
I would also try a couple of good quality directories (ensure they are manually edited directories and don't look like link farms). Remember though, don't do too many directories - especially not to start with!
From here I would recommend writing a press release and getting it published around the web. Obviously the first press release should be titled something along the lines of "New Website Open For Business".
After the press release, ask a couple of friends (or even better - customers) to write a review of your website on a review site. Once you get a couple they start looking legit but don't go over the top!
This should get you hopefully a few links. From here-on you should start picking up skills and learning more about how to get better links and optimise more efficiently.
I would recommend that throughout this whole stage; every single one of your links uses branded anchor text (or naked anchor text). What I mean by this is use yourdomain.com or click here etc).
Hopefully this helps?"
I feel your pain, Steve! Unfortunately these things take time. If you havent already, whip up a spreadsheet of all the remaining bad links. Add a column to explain what steps you have taken to get the link removed. Google will understand that sometimes you are not in control but you can only try. They might help with manual interventions. You can then use this spreadsheet to send them to ask to be reconsidered. It is important not to keep sending the request, fix the problem and then ask. Remember that they don't owe you anything so don't depend on this method - chances are they might not even reply!
Google have announced that a tool could be coming out soon which will allow you to tell them which links you wish to distance yourself from. Keep an eye out... Clicky.
In the mean time, don't just work on removing these bad links, concentrate on building much more good quality links in a variety of forms. Try and make your link profile look natural - over time these things will help.
On a side note, you need to add a canonical tag to your home page. Your domain loads a different homepage for http://www.yourdomain.com as well as http://yourdomain.com.
Check out the attachment to see why your link profile is so un-natural. You have 8220 links from ONLY 78 domains for one anchor text and 4047 links for another anchor text while your domain name only has 188 links.
EDIT: You haven't actually been de-indexed (see attached) so you don't need to submit reconsideration yet. You just need to sort that link profile out BADLY first.
As a token gesture to help you out in your time of need I have added a contextual link from one of my websites to your homepage with the anchor text "click here" - its a small drop in the ocean but every little bit helps make your profile look that tiny tiny tiny bit better.
Erm. I'm a little confused here. Is this a joke? Are you saying that you have stolen your competitors content and added it to your own website? 
The two words "unique" and "cloned" certainly do not go hand in hand. If you have copied somebody's unique content then it is no longer unique and certainly will not help you in the slightest!
Hopefully I read your question wrong but after re-reading, I can't see where I might have misunderstood.
EDIT:
Actually, having investigated a little further it appears that you have actually copied somebody's website design and added your own content. Can you confirm that this first link is yours and the second is your competitors?
http://hemorrhoidssuccess.com/
http://hemorrhoidtreatmentadvice.org/
I would question the need to clone a website, especially one which looks to be targeting English speakers with a look, feel and design which looks like it has been made by buying by a Fiverr.com gig from an oversees design company... Why not build your own? I have nothing against websites built oversees by the way - it just seems that there are so many poor ones out there!
Some good tips here to get you going. The key is to try and keep your link profile as natural as possible while concentrating on quality. Its not easy...
I would be careful about doing too many directories to start with, maybe pick 3 or 4 at the most. When your link profile gets better you can then come back and maybe do a few more.
A nice press release saying you have a new website would work fine too. Get it distributed around the web and this should build a couple of links. Again, don't go OTT with press releases, keep them to a minimum but it will give you a decent start.
I did a similar thing not too long ago (maybe 9 months ago) for a friend. To cut a long story short he only usually averaged 50 visitors a day coming on to his website from Google and about 400 visitors as direct traffic. He ran a large scale offline marketing campaign and the printers managed to screw up his domain name so he wanted to do the same thing as your client.
I anticipated a similar effect to what you expect in that SERPS might drop slightly but then recover. However, his 50 visitors a day dropped to around 25 a day for 3 months and all his rankings (not that there were many terms he ranked for anyway!) dropped off quite badly. After 3 months, they recovered quite well apart from one search term.
I think on a larger scale operation such as yours, the data and figures might represent a real life answer a little more than my data set on such a small scale website... Due to this its hard to say whether you will see a similar effect on your clients website.
It's OK. Panic over. I thought you were saying that you had copied somebody's content.
I would recommend starting at the bottom. I wrote an answer to a similar question not too long ago:
http://www.seomoz.org/q/first-links-for-a-new-site
One thing to remember is to think naturally. If you are looking at starting link building projects then always question whether the methods you are using look authentic and organic.
One last thing to remember, please don't ask people to write fake reviews of your sites and/or products. Don't take shortcuts in SEO or you will get stung like the millions of other sites using the same tactics as you. The chances of getting anybody on SEOMoz to partake in questionable methods is pretty low (or actually nearly impossible).
You have given me an idea for an article, thanks. I think I will monitor this one for a few months and see how it goes 
I'm assuming by taking them offline you mean discontinuing the product permanently? If so, it is important that you 301 redirect (always 301 redirect unless the product is coming back at some point) the page to the nearest closest product or if there is nothing similar that you sell, redirecting it back to the closest category page.
Hope this helps a little?
Matt
That's not the site I was talking about specifically but it is a site that my team are working on.
Looking at that product on your page, the content is essentially is a list of features. My advice? Try and make it unique and interesting. It can be hard to do this without simply thickening the content with fill words though. Maybe try to be funny?
By the way, I'd try and make your URL a little shorter 
Matt
I'll admit to not being too familiar with their service but after looking on their website I still can't tell what methods they use to "gett you to rank 1" (in their own words).
Smells fishy to me instantly.
This should help you out Josh:
You need to set up pagination correctly.
Alternatively, altering how many products are on the page might help but don't do this if you think it might effect your customers experience (although unlikely).
The most important thing to think about here is your visitors and not the search engines.
Imagine being a customer and searching for "log house prices". Chances are you will want to see a list of prices. This lends itself to the category page perfectly. I would imagine that seeing an article or content page would have a higher bounce rate and will most certainly have a lower conversion rate (for this keyword at least).
Remember that there is no reason not to have a nice bit of content on the category page if it adds value to your visitors.
With regards to the term "log houses", this could be used for a more generic page which covers your entire range. This decision should be based on how much time you have to spend on the website, your resources and more importantly, the competition for the keyword. If you feel like you can rank for that term instead of log house prices then go ahead and give it a go... It will be harder though, that's for sure.
Matt
WOW. They are using some SERIOUSLY OLD techniques. They have incredibly aggressive and poor link building methods, all based on exact match anchor text links and all from horribly poor domains mostly built to serve the purpose of creating links.
You will be safe in the knowledge that their rankings shouldn't last long at all - hopefully!
You should noindex your tags, yeah. All the post snippets are just duplicated content. There are loads of other stuff you should also noindex. If you haven't already, install the Yoast Plugin. There are loads of guides online on how to set it up to block the correct pages.
I see a problem already, although it could be that these links have been disavowed (there is no way something like Open Site Explorer can tell this).
Check out the image attached. You have used some very aggressive link building tactics which target exact match anchor text links - and lots of them! Very unnatural indeed.
Can you confirm that these have been disavowed?
Matt
If the pages are worthwhile sharing you could always use the medium of Google+.
Any link shared on G+ gets indexed pretty damn quickly... Quick tip, they also carry PR
Check out this useful cheat sheet:
http://googlepluspagerank.blogspot.co.uk/2013/04/googleplus-post-link-cheat-sheet.html
Just remember not to just drop shameless links though, try and involve them in discussion and community. Encourage feedback and conversation
Alternatively, there are lots of other ways of getting a page indexed.
The opposite side of the coin needs to be looked at though. There could be a reason why the pages **aren't **being indexed. Are they duplicated content? Have a canonical source? Duplicated titles? Thin content? Bad page link profile?
Hope this helps?
Matt
mmmmmmm.... I like Vanilla!!
My life would be complete if Google decided to do that!
Hmmm, I understand. It can be frustrating.
The problem is that even if you are trying (and trying hard) to sort the issue out, if they still see bad links they wont lift any manual penalty.
I'm not saying that it is worthwhile in your case but sometimes it can make sense to throw away a domain and start again. Does it take many sales?
Just remember that if you start again with a new domain, do it properly and don't outsource to people who can't be trusted
SEOMoz updates its ranks once a week usually - rankings change daily, sometimes hourly. This could be a factor.
Also, ensure you have the search engine selected as your localised Google within SEOMoz.
As a side note, ensure that you block cookies, use incognito and aren't logged into any Google service. If you are, it will give you personalised results.
You can install Wordpress on the same domain on a page like mydomain.com/news
Blogs can be a great source for gaining visitors and also keeping your website's content fresh.
Also, with regards to blogging on other sites or your own site, I wouldn't assume you should limit yourself to one or the other - do both As long as you blog on other sites and build natural looking links then this should help your site rank better and in a safe way.
Don't underestimate the role that a blog can play in building links to your site. If the content is good, you might find some natural links firing your way but even if this doesn't happen you can build links to your blog posts manually which would then send "juice" through the rest of your pages
Matt
Whether you should disavow them depends on whether they were actually bad links and whether you are under the web spam teams microscope. Have you received any messages from them? Do a bit of research into the domain the link is coming from and its own link profile.
Also bare in mind that if the link is no longer there, they will automatically be removed from Webmaster Tools eventually anyway.
Matt
This is definitely a thin content issue. Your drop in visitors coincided with the Panda 9.3.1 algorithm update. This update targets thin content specifically.
Looking at your product pages, they are incredibly sparse and contain little content. Content is one of the key (and most important) factors to getting your pages ranking.
I would recommend looking at further issues with the website which should also help:
Can you confirm whether you received a message within your Google Webmasters account?
Hope some of this helps.
Matt
Tough to explain where you should start with this without a 10,000 word reply.
It sounds like you might benefit from reading this... http://moz.com/beginners-guide-to-seo
Once you have read that, there are a few other things you need to do before thinking about building some nice, relevant and natural looking links.
There are loads of other bits to do but these are certainly something which will help you on the way.
Before answering, it's important to understand your motive for removing 100+ pages from your site.
In some instances, removing pages could actually help your site if the quality of those pages is poor, the content is taken from elsewhere, or if they are relatively thin pages.
There are lots of other questions, too, depending on your answers. Would you mind sharing the URL's in question?
