It's hard to say also that it MUST be the store being affiliate. I've heard the affiliate argument for 13 years and in the past when we had issues (Big Daddy we didn't have the canonical URL) everyone was saying it was affiliate links. We fixed the www and non www and we bounced back with no problem. It's just hard to swallow that we are basically done because of our store. That means it's over and there really can't be anymore small businesses that can't afford their own inventory.
I'm not focused only on the 404's. I am open to suggestion but at the same time, if I just accept it's affiliate store then it's time for me to shut down the server and roll over. Which might very well be the case but shouldn't I be exploring all suggestions? This has been my sole business for 13 years. It's not like I am webmaster of several sites and if it goes down, then I move on.
So, I am just seeing what all the ideas might be out there so we can explore more. In case we have missed something.
In fact, we weren't assuming it was to do with 404's all this time considering that is what we were told to do on the Google forums as we didn't have smart links to 301 to. We were assuming it was because we changed 25,000 links out of a ~80,000 page website.
Also, if it was just to do with the affiliate pages, then why is the rest of the site slumped? Again, not as badly but still slumped.
Sometimes it's not an obvious problem and so I came here to hear any and all ideas. If I have to throw in the towel because I have an affiliate store, then I guess I have to do that.