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Yes, the on-page optimization tool is up to date with Google's recent updates.  You'll notice that the tool will call out when you have over-optimized or keyword stuffed content.  Because the on-page tool doesn't look at inbound links, however, getting an A+ in the tool won't mean that you are safe from Penguin penalties - make sure to be checking your inbound link profile as well.

EMD = Exact-Match Domain. There are some Penguin cases where if you had a domain like "makemoneyonline.com" AND you were aggressively targeting "make money online" in inbound anchor text, you could run into trouble.

I think the crawl tets tool might be able to help you, it outputs a csv with some of the info. http://pro.seomoz.org/tools/crawl-test

Wanting a quick fix with is what got you into the mess you  are in in the first place. Maybe consider not doing more of the same Do something amazing and get lots of brand links

Dealing with p1, p2, p3 within a blog. Would the following deal with the duplication? name="robots" content="noindex,follow"> Or would using the rel="next" and rel="prev" work better?

Thanks will take a look at this!

The first website is not too bad, it seems to have many pages, I mean social links are not advisable but they can work depending on the style. I also had a quick look at the backlink profile seems they use related sites, articles in mass, blog comments, forum posts, I mean not the best but it seems to work! But for how long? The second website the content is lower, yet it seems to provide something the "a limited amount of" users want. Don't get me wrong I have had 1 site removed from the index for no reason at all deemed low quality so when I see junk like this it makes me angry, but I feel the first site does serve its place and Google search quality would probably let it slide, the second site however I do not know how long it will last it is just a matter of Search Quality finding the sites.

I strongly doubt that checklist is enough to tip you over the edge - it could just be that the page is code-heavy relative to any unique content (we including the template text in our duplicate calculations, so sometimes it can be over-sensitive). If there's no unique information at all, then I'm with @MyHolidayMarketing - the time to add unique content to 30-40 products is time very well spent, for both SEO and conversion. If the problem is that you're spinning 30-40 products out into 1000s of URL variations, then you may want to consider not indexing all of those or canonicalizing them. Having every color and size of every product in your Google index can start to devalue your core pages after a while. That really depends on the scope.

Hi, I admit, it does sounds spammy but the way it's been designed its not really as it's like a drop down list and not just a straight list of 200 blue ugly URLs lol. Thanks for your time

Yes that would be better, or just trying to go for "Builder" with out a location.