After these things are fixed, the thing you can do is to write Google and explain your situation, what was done, it is now fixed and ask them to lift any penalties or restrictions on crawling. At least the site has a decent PR and is not grayed out.
As for the cookies that Matt B mentioned I can definitely tell you that if the site requires that one accept cookies, that will hinder crawling. We have a client that if you do not accept cookies, you are redirected to an ugly page that says you need to have cookies to see site. You cannot even view the home page. They started doing this about 5 months ago for God only knows why and because of it, have just absolutely dropped out of site in all crawlers. They perviously enjoyed pretty good rankings. All attempts thus so far to get them to change this strategy has been fruitless.
Also after all the "spam-iffy" issues are fixed, you may try a direct feed into Froogle to get those product pages listed. I wouldn't do this though until the issues are corrected and you are able to get some kind of feedback from Google on the history of the domain.
Good luck with it, looks like you have your work cut out for you.
I wonder who got them into the trouble that is mentioned in the case study. Mmmm...










