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Hi John, There is no hard and fast rule. When the number of internal links become unnatural, or when the purpose for having those links one page becomes unnatural, then this is when they are too many. Hope this helps!

Hi John, Question: When you say WMT reports 421 instances of "pharmacy" - where do they report this? In your inbound anchor text, content keywords, or somewhere else? Also, does Google report any malware on your site? I couldn't tell from the question. Regardless, if you're unsure about any lingering hack, I'd use a tool like Securi to do a site check. If you're site is indeed clean, I wouldn't worry too much about the latent data in Webmaster Tools. But if you're site was infected for a long time, you can try filing a reconsideration request which might prompt a set of human Google eyeballs on the site. If you site is clean, you can also perform a "crawl as google" and submit all linked pages to the index. Hope this helps! Best of luck.

You should get an Advanced Google Analytics Consultant to figure out what is happening. I know if I were in this problem, I would be running a lot of Advanced Segments. Every business is different so there's no canned responses. Also the reason I say to hire someone for an analysis is if what you say is true and you don't believe the site has a penalty, then you can be losing traffic for many other reasons. You need to find out "why" conversions are lower.