FTR, I am watching this thread with interest. I picked up a very nice 4000D system without SCSI and am now taking the time to do some IDE stuff. I have been repeatedly successful with my 1200's IDE, but the 4000's seems to be a little more cranky. I may have determined the problem is with the actual drive I am using (a KingSpec 64GB PATA SSD) but I have more experimenting to do.
Essentially, I am starting from scratch with OS3.1 and then upgrading 3.9-BB1-BB2. No WinUAE for me, though. So you can't post up too much info, IMHO.