The good news is we never had spammy content on our site. EVER.
The bad news is, we are talking nearly 25,000 pages and there is no way on earth I would be able to remember what pages should go where. We do not have direct matches from old to new. Basically we let go of our old affiliate and replaced it with a new one. Therefore, no direct match redirects. We had been advised on the Google boards that the last thing you want to do for the bot or for people is to let someone looking up one brand item and then plopping them on a completely different brand and MAYBE an item of similarity. That was a maybe. So no, it wasn't spam but everywhere we read, a 301 on something that doesn't very closely match is not good either and that it sends the wrong message to the bot. Not to mention people. We also had questioned then could we just send them to the front page. We were advised not to do that either with that many pages.
But then again, I guess we aren't supposed to be designing sites for people anymore. :/
So I guess since we are talking thousands of pages that have no logical home, we are pretty well screwed.
I guess the rule of thumb here is even if an old affiliate supplier is screwing you over, if you are ranking, never change your site. This has been a most depressing thing to have found out. We were miserable being treated so poorly, now we are miserable because our 13 year old site is suffering for our store.
The rest of the site does alright still. Which is weird. It's not AS strong but it's not completely dead. Problem is most of our sales came from organic search results.
Very sad. Thanks for the input.