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ouch.  If I understand what you just communicated, you've got a site that had previously worked with the www version, but now, due to technical changes, the www version doesn't function?  And won't for a couple months?

That's a scary scenario and having worked with many different developers and systems administrators over many years, I've never allowed one to tell me "we can't fix that for a couple months" and get away with that claim.

It can either be addressed or it can't at the site level or the server level, one way or another.  Regardless of development framework, you should be able to set the non-www to redirect to the www version at the server level and it should work right.  If there's a massive bug in the Magento implementation, that sounds like a very serious flaw in the developer's skill set as far as I can tell.

So - IF you're stuck, you're going to have a major SEO problem for longer than a couple months.

By all rights the only solution in that scenario is to scrap the www version altogether and NOT revert back to it in a couple months.  Change all the 301 redirect settings and within GWT to now point to the non www version.  Then work to build up more links to the non www version over time.

Because that's the only short-term solution you can do now from a best practices approach if the failure can't be quickly addressed.

And down the road, if you do this, you'd have to once again reverse everything, just causing you more problems.

So either get a developer / IT specialist who can fix it immediately, or scrap the www version altogether.

The question is this - why would you want to keep Site A given the current insurmountable challenge you describe?

Do you still hope there's some value in it being kept alive?

Do you still hope there's some SEO value or that the site will or does continue to bring some traffic you believe to be valuable?

Because (and this is just my opinion) if you are convinced you cannot or will not (for whatever reason) work to clean the mess up, you'd be better off completely killing off Site A.

If you don't even if you migrate site B to a different server, the links still exist. The footprint remains.

If Site A is a cash cow that does not need SEO, then I would block the entire site from search engines via robots.txt file.  Even on separate hosts, all the links pointing to Site B are a big negative due to the sheer volume, given that there's likely a "bad rap" label associated with SEO on site A.

Duplicate content does not need a "same server" relationship to be a big problem either.  All duplicate content is a problem regardless of location.

If a client I represent is doing things that I believe are impeding their success, I personally believe it's important to communicate my concern. However, if they choose to ignore that communication, that's their right to do so.

This is a sad reality that many business owners face.  SEO is a very complex process and unfortunately it's a case of two-fold barriers to success.

On the one hand, not all SEO's really know, or even if they do, don't consider long-term ramifications of what they might be recommending.  Many of us in the industry think and act otherwise, however it is a problem nonetheless.

On the other hand, Google constantly changes their rules to a certain extent - as more people look for ways to game the system, what may have been acceptable previously can become unacceptable as Google tries to clean up the mess.  It's a vicious circle.

So...

You can get "rid" of indexed pages by blocking them through a robots.txt file - if there are patterns to their URLs.  if it's an entire site, you can block the whole site in one line in the robots.txt file.  If it's multiple sections of a site, you can block entire sections while leaving other sections open for search indexing. A professional should be tapped to help you with that.

Its important to consider whether pages should be blocked, or instead, redirected to other pages that you want indexed or are indexed that are similar in nature.

Bad link evaluation is a professional process and should not be undertaken lightly.  In many cases, site owners will ignore your requests, so it's important to at least get the request process right and to document the process. Again, a professional is needed for that.

And yes, you can submit a request after that's done.

Unfortunately, anyone you task to do the work that would be able to help you will both charge you for their time and cannot guarantee that what is done will be enough.  It's another reality of the world we operate in because Google cannot reveal trade secrets to help you know what exactly needs to be done.

site:trophycentral.com -www  shows all content indexed not within the www subdomain.

I recommend implementation of Google's Rel-Publisher markup - to designate the original publisher.  There's at least one WordPress plug-in for this however I can't speak to whether it works or not - only that the Google markup is currently best practices...

Combined with Rel-Author, it's how Google determines content ownership

yes, inbound links are those coming from other sites - and quality is important there- as well as diversity, both in the types of links as well as ensuring to keep the majority of links coming from as many independently separate domains as possible.

It's correct that you can't directly control or dictate which pages Google includes in sitelinks.  You can, however, help influence this by better optimizing the pages you want included through more emphasis on your brand within the content of those pages - integrate brand references within on-page content.  Then, work to get a mix of brand-centric anchor text into links coming from other sites that point to those pages.

It's not a guarantee, however I've seen some success in this method for various clients.

The more emphasis, signals and depth of content, supported by a stronger individual page focused inbound link effort, the more likely the pages you care about will be to end up in sitelinks.

There isn't one formula unique to sitelinks that Google specifies, so I've only ever just applied best practices SEO concepts to my desired goal.  And have seen those pages sometimes become sitelinks.

bitly is one of the most well established shortener services available.  They provide click-through data across several data points.  This helps site owners track the relative success or shortcomings of content they wish to promote, and can be used to determine what works and what doesn't from a marketing and promotion perspective.

there are many ways to track traffic, however if you use a shortener service like bitly, you get a shorter URL for easier / cleaner distribution, you can rapidly evaluate a specific URL's performance tied directly to a specific marketing campaign method, and when other people spread that shortened link, it's just as effortless to track click-through for that specific initiative regardless of how many times that is shared.  Much easier than digging into analytics and setting up unique campaigns.

It is of course, far from perfect, and there are many ways to get the data - bitly is just one and it's handy.  Especially with the functionality of generating the unique shortened URL on the fly which is much faster than setting up custom tracking campaigns in GA.

If you know that they were valid pages, and if the relevance of the no-longer-existing pages matches relevance on specific pages on the new site, set up 301 (not 302) redirects at the server level to regain some of their previous value.

If you are unsure of their value, or there is no relevance match, you can use Google Webmaster Tools to have the pages removed from Google's index.

Rel-Canonical is a signal.  While it helps mitigate problems of duplication, it is just one signal.  If enough other overriding factors exist, Google's automated ability to "figure things out" can become weak and confused.  So for example, if all of the pages are linked to from multiple points within the site, or if any of that content is linked to from outside the site, there could be negative impact.  It's not supposed to occur, however it can due to imperfect layering of multiple algorithms.

Ultimately, there may be a need to block some content more forcefully, such as via robots.txt file.  Unfortunately there's no definitive method for evaluating this specific issue in an isolated manner without serious live site testing over extended periods of time.  So my recommendation to clients is to not mess with it unless you've seen a serious drop in organic results, and only even consider testing if you can't identify other potential primary causes.

Structured data is extremely beneficial when executed properly and under the right circumstances. It's not usable for every single piece or type of content on a site though.  So the first challenge is to determine what on your site is viable for being coded with structured data markup.

For example, on the article you referenced, Google gives some examples of the types of content that would benefit from this:

• Reviews
• People
• Products
• Businesses and organizations
• Recipes
• Events
• Music

There are many more uses nowadays - article authorship information, publisher information, and a host of possibilities thanks to Schema.org - a collaborative effort between Google, Bing and Yahoo.

Want to go even further, you can then layer in the Facebook OpenGraph system on top of that - a completely different way to markup content information for crawl-ability improvements.

As you scan through all the various types of data that could qualify, from there it's a matter of following implementation guidelines.

If you've done any type of search recently for sports scores, weather, searches with "reviews" in the search phrase, "Current events in ____", you've likely seen structured data integrated into some of the organic results - when you see it, it's pretty obvious in that it provides very specific types of information, presented in very clean visual ways as compared to purely seeing a page title and two line description of the page.

It's not just the "average position" that matters - total number of impressions is a critical consideration in understanding what's going on.  When you've got less than 50 impressions, it means that your listing showed up in results less than 50 times, regardless of position (not all instances necessarily had a particular entry in the actual #1 position).   It's not unusual for a new site or new content within an existing site to fluctuate in rankings.

Google has several algorithms - as one is run, a particular page might be placed in a certain ranking position temporarily.  Then when another algorithm is run, the results could impact the original placement up or down.   Over time, part of the process also includes Google varying placement in order to gauge reactions - if not enough people click on a listing in a certain ranked position, that will further impact results the next time a similar search is performed.

The key is to to focus on the longer-term experience and steadily build signals to reinforce "this page deserves to be ranked highly".

If the information contained in the academic policies is not needing to be kept confidential, and if that information is valuable to students (or even perhaps people considering becoming students, or parents of existing or potential students), then for those reasons, it would be legitimate to make it accessible from the main site without them having to go hunt for it.

Given those reasons, I believe it would be perfectly valid to have it be crawlable and indexable by search engines.

I would also group it all together in a dedicated location (such as a sub-folder hierarchically) with it's own sectional sub-navigation because it's no different than any other quality content - grouping topically focused similar content is proper for user experience.

As for the student profiles that's a completely different issue.  This one involves the reality that it is most likely most student profiles are going to have very little depth of unique content.  I assume students will fill out the content themselves. That leaves the door open for all sorts of good, bad and ugly.

Further, if there is some reason for students, faculty or other staff to be able to access it without having to sign in to a secure area, that is not a reason to have it found in search engines.

There are privacy concerns (so a secure area is then in fact, the best option if that's the case).

Most likely being "thin" or even some low quality or perceived duplicate content, if it's not hidden behind a log-int, it really should be blocked from search engines in a robots.txt file or use noindex,nofollow meta tags.  (no valid reason to do noindex,follow).

Having said all that, I would suggest it could just as well go in a sub-folder of the main site or a separate sub-domain.  Since it will be blocked from indexation/crawling, either would work.

One final reason it shouldn't be indexed or followed is as students come and go, that way you don't need to worry about a "301" redirect system to deal with them.

Yes this can definitely affect SEO.  When I go to the site, without using https, it automatically redirects to the https version, and that gives me the error.

So the question is - does the version of the site the public sees have to be in https (secure) status ? If not, I would suggest having that removed as soon as possible.  Have the public version work without it and set up a 301 redirect.

If the secure version is required, I would contact the site systems administrator as soon as possible to get it resolved.

so the answer is definitely "the certificate needs to be fixed as soon as possible because every day it is not, nobody can get to the site. That will then cause the SEO to fall apart. The longer it's down, the longer it will take for search engines to reset once they devalue the site."

This confirms the need to get an expert involved - one experienced in these types of issues - a programmer or systems administrator type expert, not necessarily an SEO expert.

It's all at Google's whim - no way to directly control it.  They're only earned when a site is perceived to deserve the trust within its content focus, so take it as a positive.  And be aware they may change how/when they display them without warning.