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Hi Mozzers, <a>http://www.alivenetwork.com/ </a>is a close competitor of ours. They're ranking far better than us even though many of our search metrics are the same...except one! links! To give you an idea, we've got a fairly large backlink profile for the industry with quality links.
34,981 links from 276 Root Domains = about 127 links/domain. Alive Network has 1,692,256 links from 705 root domains = about 2400 links/domain. Surely that looks a bit black-hat right there? Is it just a matter of time until they're penalised? Perhaps they're just a bunch of domain-wide links? Thoughts would be appreciated.

Hi Mozzers, We've recently updated a site of ours that really should be doing much better than it currently is. It's got a good backlink profile (and some spammy links recently removed), has age on it's side and has been SEO'ed a tremendous amount. (think deep-level, schema.org, site-speed and much, much more). Because of this, we assumed thin, spammy content was the issue and removed these pages, creating new, content-rich pages in the meantime. IE: We removed a link-wheel page; <a>https://www.google.co.uk/search?q=site%3Asuperted.com%2Fpopular-searches</a>, which as you can see had a **lot **of results (circa 138,000). And added relevant pages for each of our entertainment 'categories'.
<a>http://www.superted.com/category.php/bands-musicians</a> - this page has some historical value, so the Mozbar shows some Page Authority here.
<a>http://www.superted.com/profiles.php/wedding-bands</a> - this is an example of a page linking from the above page. These are brand new URLs and are designed to provide relevant content. The old link-wheel pages contained pure links (usually 50+ on every page), no textual content, yet were still driving small amounts of traffic to our site. 
The new pages contain quality and relevant content (ie - our list of Wedding Bands, what else would a searcher be looking for??) but some haven't been indexed/ranked yet. So with this in mind I have a few questions: How do we drive traffic to these new pages? We've started to create industry relevant links through our own members to the top-level pages. (http://www.superted.com/category.php/bands-musicians) The link-profile here _should _flow to some degree to the lower-level pages, right? We've got almost 500 'sub-categories', getting quality links to these is just unrealistic in the short term. How long until we should be indexed? We've seen an 800% drop in Organic Search traffic since removing our spammy link-wheel page. This is to be expected to a degree as these were the only real pages driving traffic. However, we saw this drop (and got rid of the pages) almost exactly a month ago, surely we should be re-indexed and re-algo'ed by now?! **Are we still being algor****hythmically penalised? **The old spammy pages are still indexed in Google (138,000 of them!) despite returning 404's for a month. When will these drop out of the rankings? If Google believes they still exist and we were indeed being punished for them, then it makes sense as to why we're still not ranking, but how do we get rid of them? I've tried submitting a manual removal of URL via WMT, but to no avail. Should I 410 the page? Have I been too hasty? I removed the spammy pages in case they were affecting us via a penalty. There would also have been some potential of duplicate content with the old and the new pages.
_popular-searches.php/event-services/videographer _may have clashed with _profiles.php/videographer, _for example.
Should I have kept these pages whilst we waited for the new pages to re-index? Any help would be extremely appreciated, I'm pulling my hair out that after following 'guidelines', we seem to have been punished in some way for it. I assumed we just needed to give Google time to re-index, but a month should surely be enough for a site with historical SEO value such as ours? 
If anyone has any clues about what might be happening here, I'd be more than happy to pay for a genuine expert to take a look. If anyone has any potential ideas, I'd love to reward you with a 'good answer'. Many, many thanks in advance. Ryan.

I can't help but feel this is a somewhat untapped resource with a distinct lack of information.
There is a massive amount of information around on how to rank a new website, or techniques in order to increase SEO effectiveness, but to rank a whole new set of pages or indeed to 're-build' a site that may have suffered an algorithmic penalty is a harder nut to crack in terms of information and resources. To start I'll provide my situation; SuperTED is an entertainment directory SEO project.
It seems likely we may have suffered an algorithmic penalty at some point around Penguin 2.0 (May 22nd) as traffic dropped steadily since then, but wasn't too aggressive really. Then to coincide with the newest Panda 27 (According to Moz) in late September this year we decided it was time to re-assess tactics to keep in line with Google's guidelines over the two years. We've slowly built a natural link-profile over this time but it's likely thin content was also an issue. So beginning of September up to end of October we took these steps; Contacted webmasters (and unfortunately there was some 'paid' link-building before I arrived) to remove links 'Disavowed' the rest of the unnatural links that we couldn't have removed manually. Worked on pagespeed as per Google guidelines until we received high-scores in the majority of 'speed testing' tools (e.g WebPageTest) Redesigned the entire site with speed, simplicity and accessibility in mind. Htaccessed 'fancy' URLs to remove file extensions and simplify the link structure. Completely removed two or three pages that were quite clearly just trying to 'trick' Google. Think a large page of links that simply said 'Entertainers in London', 'Entertainers in Scotland', etc. 404'ed, asked for URL removal via WMT, thinking of 410'ing? Added new content and pages that seem to follow Google's guidelines as far as I can tell, e.g;
Main Category Page Sub-category Pages Started to build new links to our now 'content-driven' pages naturally by asking our members to link to us via their personal profiles. We offered a reward system internally for this so we've seen a fairly good turnout. Many other 'possible' ranking factors; such as adding Schema data, optimising for mobile devices as best we can, added a blog and began to blog original content, utilise and expand our social media reach, custom 404 pages, removed duplicate content, utilised Moz and much more. It's been a fairly exhaustive process but we were happy to do so to be within Google guidelines. Unfortunately, some of those link-wheel pages mentioned previously were the only pages driving organic traffic, so once we were rid of these traffic has dropped to not even 10% of what it was previously. Equally with the changes (htaccess) to the link structure and the creation of brand new pages, we've lost many of the pages that previously held Page Authority.
We've 301'ed those pages that have been 'replaced' with much better content and a different URL structure - http://www.superted.com/profiles.php/bands-musicians/wedding-bands to simply http://www.superted.com/profiles.php/wedding-bands, for example. Therefore, with the loss of the 'spammy' pages and the creation of brand new 'content-driven' pages, we've probably lost up to 75% of the old website, including those that were driving any traffic at all (even with potential thin-content algorithmic penalties). Because of the loss of entire pages, the changes of URLs and the rest discussed above, it's likely the site looks very new and probably very updated in a short period of time. What I need to work out is a campaign to drive traffic to the 'new' site.
We're naturally building links through our own customerbase, so they will likely be seen as quality, natural link-building.
Perhaps the sudden occurrence of a large amount of 404's and 'lost' pages are affecting us?
Perhaps we're yet to really be indexed properly, but it has been almost a month since most of the changes are made and we'd often be re-indexed 3 or 4 times a week previous to the changes.
Our events page is the only one without the new design left to update, could this be affecting us? It potentially may look like two sites in one.
Perhaps we need to wait until the next Google 'link' update to feel the benefits of our link audit.
Perhaps simply getting rid of many of the 'spammy' links has done us no favours - I should point out we've never been issued with a manual penalty. Was I perhaps too hasty in following the rules? Would appreciate some professional opinion or from anyone who may have experience with a similar process before. It does seem fairly odd that following guidelines and general white-hat SEO advice could cripple a domain, especially one with age (10 years+ the domain has been established) and relatively good domain authority within the industry. Many, many thanks in advance. Ryan.