Boy this is a tough one. I won't take sides here because you are both stand up guys. Andy has helped me and spent many hours trying to get my PCV set up. He really went out of his way driving over an hour each way to my house to help many times. I can tell you that the motor ran great before it was sent to you. I don't think Andy would have ever sold anyone a motor that had issues if he knew about them. You seem like a great guy and always willing to help people when they need it as well. I think this situation sucks for both of you. I don't know what I would do if I was Andy because when we buy something used it is as is with no warranty unless it was agreed to prior to the sale. With that being said if I was in your shoes I would be very angry and let down. This is going to be something you two will have to work out and settle and I hope it turns out good for both of you.
As far as the new secondary I would absolutely rebuild with the new parts. Send a message to Matt he has a lot of knowledge about this since he just went through it. Don't waste your time rebuilding with the old secondary. It will be a never ending battle. Sorry to hear about your misfotune I truly know what you are going through. Let me know if I can help you out with any phone numbers or part numbers or anything you may need help with.
2009 Prowler XTZ 1000 with a few modifications. Needs paint & powder coating.