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Please see answers in Bold.

1. is the bottom content ok? please scroll down all the way. --- **The content is good. It should help your homepage rank for a lot of long tail keywords, provided it's optimized for them. **

2)  We used semantic keywords for 5-6 anchor interlinks to the same page to promote core products from the home page.  Is this too much? - Anchor Texts to the same page won't help. If I were you, I would rather send 5-6 important links to the most important (different pages). Multiple links to the same page from your homepage won't help IMO.

3)  We repeated footer path the same as the header fly window (same link, same word), is this over-optimized?  If not, does it serve any SEO? -- I don't understand this part of your question.

Is your site brand new or relatively old/established ? If it's relatively old/established, do you really care about the extra 30 uniques a day from 30 domains ? If it's a brand new site, relatively new(ish), and it does not have a link profile of it's own, I'd probably not do it. It just sounds scary.

However, going back to if you are established and have have  strong domain authority, link profile, redirecting domains is not an issue. EG, Apple.com has tons of domains that redirect. Some of them have lots of history in the SERPS. Think of all kinds of mis-spell domains, trademark domains and so on. So whatever makes sense from a usability perspective, definitely do it.

In my opinion, it's a very clear, think line.

Sebes

Are you saying there's an image "alt" tag, but no src="something.jpg"  ? That is a the darkest shade of gray if not completely black hat. I would definitely avoid it. This is a classic, simple, easy to detect case of over optimization, whatever else you may want to call it.

I would strongly suggest not to do it. We are in 2012. This might have worked in 1997 when Google was just born and it was primarily Dogpile.com and Altavista.com

Get them cleaned.

I would analyze the top 10 competition not just your head keywords but also some long tail keywords and find opportunities.

If you look at your rankings for keywords like, I think it's also about making sure your pages are properly optimized. See your SERP ranking for https://www.google.com/search?q=medical+plaques

I would recommend using the http://pro.seomoz.org/tools/on-page-keyword-optimization/new tool here at SEOMoz to identify some oppurtunities and strengthen your on-page.

As far as Off-page is concerned, I would recommend you to be very careful and do some strategic link building instead of the outright link buying. There's a considerable risk involved. What you need to do is build domain authority, not try to rank via anchor text hyperlinks. Does that make sense ?

I see you have canonical tags in place. Considering that, I would suggest you are good. No need to setup any of those redirects. Canonical tags are in essence sort of 301's anyways, so you are all set.

As Ben and Alan have recommended, do something newsworthy. Think linkbait. However, before you do anything like that, I would suggest you look at your link profile and see if it makes sense to do something like this.

Have you been penalized for unnatural links ?
Do you have unnatural links ?

You could also have knowem.com or another agency or (DIY) signup on all social networking sites and have a lot of brand/follow/nofollow links. A natural link profile contains all kinds of links and not too many of 1 particular kind of links. I hope this ignites some thoughts and ideas.

Try this in the .htaccess file. It should work fine for sure. You don't need to manually add your website name.

<code class="htaccess" title="in your .htaccess file">RewriteEngine On
RewriteCond %{HTTP_HOST} !^www.
RewriteRule ^(.*)$ http://www.%{HTTP_HOST}/$1 [R=301,L]</code>

Depending upon the site, I have seen campaigns indexed in as little as 12hrs and as much as 48-72hrs. Again, that could also depend upon what's in the queue and what the resources available are and how big your website is.

You might also want to try the Crawl Test tool at http://pro.seomoz.org/tools/crawl-test

It usually completes pretty fast and the data is always good to have.

Well, rel=canonical will technically work fine, however in this case if you are migrating the entire site (presuming you have all pages on the old domain, going somewhere on the new domain, I would essentially setup 301 redirects from the old domain to the new domain.

I don't think you should do anything in the webmaster console. Just remove all the pages from the old domain and setup 301s from old domain to new domain. Google Webmaster Console Site migration IMO is for scenarios like you have yourdomain.net and you acquire the domain yourdomain.com and want to migrate the domain from .com to .net or if you change the brand name to yourbrandname.net or so on.

Does that make sense ? I hope that helps.

PM/Post the URL along with exact URLs that are being reported and then me or somebody else here could look at the URL and tell you exactly what's going on and what you could possibly do.

Edit: James, based on the URLs you sent me, the issue is duplicate content between yoursite.com, www.yoursite.com and www.yoursite.com/index.html and you can handle this by adding a .htaccess file to the root of your public_html/www folder.

Options +FollowSymLinks RewriteCond %{HTTP_HOST} !^www. RewriteRule ^(.)$ http://www.%{HTTP_HOST}/$1 [R=301,L] RewriteCond %{THE_REQUEST} ^./index.html

I usually never limit it. I let the content writer decide based on how / what the topic is and I try not to restrict them to a certain word count. Short article or long, it should serve the purpose it's being written for and if it's for the user, which is what it should be, it should cover the article title in the right way and do justice to it.

I hope that helps.

You could use the SEO Spider Tool at http://www.screamingfrog.co.uk/seo-spider/. The free version has a limit of 500 URI maximum but you should be good with the free version since you said you have 300 pages.

I hope that helps.

What are you using to accomplish this ? CSS ? HTML5 ? AJAX or something else ? All these technologies have a Search Engine Friendly way of doing it. It really depends how you are doing it. It sounds like AJAX to me, but could also be CSS...so..depends.

You might already have this, but http://www.awwwards.com/ is a pretty decent source. If your site is responsive design/HTML5, you could also submit to HTML5 Galleries and if it's an exclusive/custom design on a CMS, you could also submit to that CMS's galleries, eg Wordpress and so on. Just some idea starters, I hope I ignited some ideas in your head

1. Keyword Research - Making Sure the right keywords are being targeted. Identification of Top10/50/100 Keywords, Current Rankings, Competition Identification, Analysis and Comparison.
2. Site Index-ability, Keyword Targeting, Content Quality & any architecture level issues.
3. Domain Link Profile, Strength, Social & other business initiativesand assets that can drive domain authority.

Dividing the above 3 points into On-Page (1st 2 Items) and (3rd Item)

I hope this helps.

I think you have answered the question yourself and you already knew that "I guess there is no solution to it except to find lot of other high value links myself - so not so much a question as a comment really! but happy to hear peoples own experiences of that sort of situation." Just keep doing what you are (building/maintaining that great content), but also spend time in reaching out to people who would want to link to you. I would also possibly add a link to us box with an easy to use HTML code that people could use to link to you.

I understand your concern. I am basing my answer based on the fact that if you don't have a robots.txt at all, Google will still crawl you, which means its an allow by default. So all that matters in my opinion is the disallow, but because you need an allow from the wildcard disallow, you could allow that and disallow next.

Honestly, I don't think it matters. If you think the way a bot would work, it's not like robots.txt 1 line is read, then the bot goes crawling and then comes back reads the next line and so on. Does that make sense ? It reads all the lines in the robots.txt and then follows the directives. But to be sure, you can do either of the scenarios and see for yourself. I am sure the results would be same either way.

I don't think it matters, but I think I would disallow first, because by default everything is an Allow.

You could also use Xenu Link Sleuth or Screaming Frog SEO.

This is not a manual response, it's actually an automated response. I would continute to build content and links to the site. I hope you explained your effort in trying to get rid of the links etc. That should take care of it. However considering the massive penalty messages sent by them, you'd wonder how long would it take for them to do anything for each one of those. Has to be something somewhat automated, but it can't be.