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So since I have nothing to lose I plan on using the remove tool, followed by the submit feature in an attempt to start over. This will remove all the garbage associated with the domain, and in 6 months I'll have nothing but clean high ranking results.
Is there anything I am missing with this theory? or has anyone successfully cleaned up their results?
Supplemental results do not really hurt. They make a mess of the site: searches, but sometimes I get traffic through supplemental results when people are searching the web for very obscure phrases. This however is only true if the supplemental URLs point to a still existing page, or are properly 301 redirected to a page with appropriate content.
My experience is that the existence itself of supplemental URLs does neither hurt nor help the ranking of the other pages of the same website, unless these supplementals contain duplicate content from other still existing pages. This is the only circumstance where I would recommend the URL removal tool.