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As soon as you place a link on a site that is site wide you have to wait potentially months for Google to crawl every page on that site, which is why GWT might still be showing the detail.  GWT is not the decider as to whether Google takes some action.

As long as you have rectified with either a no-follow or removal you are fine and have done the right thing.

I agree with Chris and I would ignore the error/warning.  The canonical does not hurt being there on the homepage but in any case it is set correctly.

What is the URL and what is the canonical tag in your head section?

Would you prefer to browse a site that is flat in terms of just providing static one dimensional information, or a hot site that is offering external resources and links to further information to give you the best experience possible?   Always think of the user experience.  Google probably knows that if you add links out within your content and in context to external authority sites you are attempting to give value to the visitor.  So if you do link out don't use no-follow, as you are telling Google you don't trust the sites!

As well as parameters mentioned you may possibly have heaps of duplicating categories, tags etc.  What I would also do is start searching Google with something like site:www.example.com/directory/ or possibly site:www.example.com/category/directory/directory/ so you are tightly narrowing down the results, switch to 100 results per page and manually look for clues.

Excellent response and advice.  My only concern was Jonathon has the impression he "should" link to the pages linking to him by how I read his title.

So my advice based on that would be absolutely no as a reaction to gaining the link, then to stand back, consider and follow your advice.

I think you mean the other way round.

If you have a new site and you get a link from an authority site the chances are that site page might (and it is a might) get crawled more often, which then leads Google back to your site and stands you in good stead for Google to crawl and index your site.  Other methods include submitting your sitemap to Webmaster Tools.

If good quality sites are linking to yours then that's great as it's telling Google your site is of value and will help with your rankings.  You do not want to link back to those pages, you want to go out and find more sites to link to you.

there is a good answer to this here - http://moz.com/community/q/reciprocal-links-4

Google will catch up with them, you can be sure of that.

The link operator only shows a snapshot and is in no way representative of the actual links.  Open Site Explorer on here will give a more accurate account of your link profile.

You also want to take a close look at your organic traffic stats and compare with the Google update dates here http://moz.com/google-algorithm-change and see if there is a pattern emerging.

I have dealt with sites that have just generally declined organically over a year or two and usually it comes down to poor on-site SEO (including possibly panda) and the indirect effects of penguin.

As I see it, even if it wasn't wrong it's good housekeeping to keep the same format throughout all possible URLs.

In your case the canonical is saying that that URL is the original.  Google won't crawl to it and is just concerned in the filename/main URL  - and if it did the 301 kicks in but there is no link value issue.   I would prefer to keep it tidy by matching the structure you want.

Books are ok,but there is nothing better than to get your hands dirty. As Steve says Beginners Guide to SEO is a great starting point.  Then when you start working on a site you soon realise there is no one size fits all and all sites have their own peculiarities, needs and restrictions.  That's when places like Moz will really help as you can research, absorb opinion, learn proper strategies and put it all into practice.

Those sites are just collections of links to sites

That doesn't sound good if you mean thin content as you are moving into the realms of Panda.  Each and every site needs to be rich with unique and valuable content.

How many URLs are indexed in Google if you use site:yourdomain.com  Has that figure dropped too?

Have you got anything in your robots.txt that could be blocking?

This sounds like your redirects are not right.  If you redirect from one URL to another you should have a 301 (or if temp a 302) header response.A soft 404 is where you redirect to the 404 page but you get a page found 200 header response (or any other response that is not 404).

What I would suggest is to remove any redirect from the removed URL/page and ensure you have the appropriate line in your .htaccess file for loading the correct 404 page when a URL cannot be found:

ErrorDocument 404 /whatever-you-name-your-404-file.htm

If you move the forum to a sub-domain you are still using a separate domain in Google's eyes.  You will have to do all the work you would do if you loaded it on to a completely unique domain - SEO, link development etc to build up the authority of your sub-domain.  Your sub-domain is disconnected from your main domain, it is a new website.

There is a list of recommended businesses via a link at the foot of the page.  Most SEO guys are now very experienced in dealing with penalty issues as it has become so common.

This blog post should point you in the right direction - http://moz.com/blog/how-to-improve-your-rankings-with-semantic-keyword-research

...if that is not your answer I would double check you have copied the field values correctly.

The goal tracking will only work with new events and not retrospectively.  If you trigger your event you will probably find it working.  The % figure when you verify the goal is just an indication of what would show up if already up and running.