You could save yourself a lot of time and hassles by downloading classicwb. Its probably been the most stable Workbench environment I've ever used (unless you install CGX4-there is a conflict there that I haven't worked out yet
Agreed. I have Classic Workbench AGA installed on my A4000 and Classic Workbench installed on my Minimig. OK, the buggering around with WinUAE is a bit of a pain, but it is worthwhile in the end. I use P96 for RTG so I haven't seen a conflict there. However, I'm having issues with my Deneb in DMA or PIO mode and my Power Flyer IDE card which I "suspect" may be related to CW, but I can work around the issues.
I wish somebody could get a licence to issue a full Classic Workbench
installation off disk that already includes the necessary OS3.x files and call it OS3.99.

I've had nothing but frustration trying to get AmiKit and AmigaSys installed on a real Amiga.