No. Goodbacklinks are one of the most important factors, as they are a source of traffic to the site, and a souce for Google to validate your site's content.

if you have a ton of good links, but the rest of the site is garbage, you probably wont get very good results. The algorithm looks at over 200 separate bits of information when determining where to rank a site. Are backlinks high on that list? Absolutely. Does that mean that you can have thin content, bad optimization and design? No.

Stating that "Backlinks are the most important factor in SEO" sounds more like a marketing phrase used by that company to sell their services.

Since you have links pointing at them both, I would just redirect the lower ranking one to the higher ranking one. 301

The one that ranks better woud be the one I would keep. Sometimes redirects and url changes can take a while for search engines to find, even if you fetch as Google.

Without having a look at exactly what is being done, it is hard to tell.

BUT, looking at it on the surface, yes, it is too expensive.

"I understand that $750 for an agency may not be worthwhile, however I will also be paying them $6,600 to re-write and keyword optimize 58 URLs, so there is more involved than only $750. Furthermore I will probably engage them for a content marketing campaign to the tune of $2,500 per month."

Setting up goals in Google analytics should not be a $750 cost all by itself. This can be acheived in about 30-60 minutes. I think you are being charged for analyzing the data, (which usually doesn't take a real long time) rather than the actual setup. This is normally absorbed into the cost of doing the SEO. Again, I'm not familiar with everything they are doing for you, but for the same job, (seo, analytics, content marketing) we would charge much less. I would like to see their proposal, to see if you are getting taken advantage of.

Spencer said it best when he stated "They easily could be trying to overcharge you if they think you can afford it." I have been involved in the industry for 12 years, worked at a few agencies before I owned my own, and this happens a lot more than you think. Seeing people get taken advantage of was one of the driving factors for me to set up my own company, and hire my own team. Just couldn't watch it anymore.

As long as the url is accessible, it doesnt matter. You can redirect from a subfolder, or using root domain.

One thing to remember, make sure you redirect both www, and non-www versions. Are you using cpanel? It makes this a super easy process. If not, let me know, and I can supply you with some htaccess rules to get you started.

*Keep in mind, all link juice is not always transferred. Generally most will be passed through, but I just wanted to make you aware.

If you are looking for a more permanent option, use this tool:
http://www.advancedwebranking.com/

This rank checker allows you to enter in your own keywords that you want to display the rank of. Better yet, it uses proxy servers so the results dont count against you. Only thing I would mention is to not run the report more often then once every two weeks, as this will make your impression count go way up.

Here is a link to a site we set up a long time ago: 
http://www.woodlandwindows.com/awr/

All the keyword choices showing up were ones that we chose. The front page listings show up in bold, so it's easy to see what is ranking, and what isn't. You don't have to have that large of a list.

Also, if you are trying to use a free platform to help, Google analytics can show you your top visited pages, which more than likely has a direct effect on your topp ranking pages. When you link your webmaster account and analytics accounts together, you can view search query and keyword ranking info.

I'm not sure what you mean by backlinks are not getting indexed.

From your description, it sounds like you added new pages to the site, and they are not showing up in results or as being indexed? 
"I Made few backlinks with my keyword but they are not getting index and it has been for 15 days."

1. What tools are you using to see if the backlink source is indexed?
2. Where did you get the backlinks from? Were they natural or paid? If they were a paid link, I'm not sure that is the best approach.
3. Depending on the importance of the source linking to you, it can be a lot longer than 15 days for Google to crawl the linking domian. They may have their sitemap set to a monthly crawl, in which case you will not see results for a while.
4. Backlinks dont get indexed based off of your site. This is a factor you cannot control. If the source is valid, and authoritive, you can link out the the page your site is linked from, and try and speed up the process.

You can use either. Google looks at hyphens like a space. I think it makes more sense to use piping (|) for your page titles, as that is more common, although I don't think there is a penalty for either. Below is a link to Matt Cutts blog for using different punctuation in URLs, I would imagine the same applys to page titles.

http://www.mattcutts.com/blog/dashes-vs-underscores/
and from the webmaster tools blog:
https://productforums.google.com/forum/#!topic/webmasters/cBikmAXlXXo

Hope this helps! I would worry more about the structure and keywords than the separator characters.

We never place a link without the site owners permission.

301 the old links to the new linking structure. If it is already a high ranking page, the link weight should carry through.

Since it already ranks high, I would keep as many elements as you can the same, unless they dont rank well and need to be improved. Make sure to do a site search for indexed pages, and redirect or create a removal request for any unatural cms-generated links. (component/SAMPLE/123456 etc)

DO NOT just delete the entire folder without seeing how many on page links still link to those pages. Check your on-page links to see if it is generated by the menu system, or if is hard-coded in the content.

Wordpress also has a few items you will want to change in the robots.txt file vs the old Joomla site.

User-agent: *
Disallow: /feed/
Disallow: /trackback/
Disallow: /wp-admin/
Disallow: /wp-content/
Disallow: /wp-includes/
Disallow: /xmlrpc.php
Disallow: /wp-
Allow: /wp-content/uploads/
Sitemap: http://example.com/sitemap.xml
Disallow: /wp-content/plugins

or you could also use this one:

User-agent: *
Disallow: /cgi-bin/
Disallow: /wp-admin/
Disallow: /wp-includes/
Disallow: /wp-content/
Disallow: /archives/ disallow: /?
Disallow: ?replytocom Disallow: /wp-
Disallow: /author
Disallow: /comments/feed/
User-agent: Mediapartners-Google*
Allow: /
User-agent: Googlebot-Image
Allow: /wp-content/uploads/
User-agent: Adsbot-Google
Allow: /
User-agent: Googlebot-Mobile
Allow: /

Hope this helps! Best of luck with your new build.

We had a discussion in the office today, about if it can help or hurt you to link back to your site from one that you optimize, host, or manage.

A few ideas that were mentioned:

HURT:
1. The website is not directly related to your niche, therefore Google will treat it as a link exchange or spammy link.
2. Links back to you are often not surrounded by related text about your services, and looks out of place to users and Search Engines.

HELP:
1. On good (higher PR, reputable domain) domains, a link back can add authority, even if the site is not directly related to your services.
2. Allows high ranking sites to show users who the provider is, potentially creating a new client, and a followed incoming link on anchor text you can choose.

So, what do you think? Test results would be appreciated, as we are trying to get real data. Benefits and cons if you have an opinion.