Well I finally got round to doing this and now I'm up and running again.
I've also got Frodo (v2 I think it is) working at 100% speed with only a frameskip of 2 . So I thought I would share my setup so others might benefit.
Amiga 1200 Viper060 with 64mb ram
First installed Amiga sys with WB3.1
Then upgraded to OS3.9
Added boing bags 1 2 3 and 4
Added the following from aminet (all after setpatch in startup-sequence)
speedychip
Newwpa8
Blazewcp
Still haven't managed to get my CD drive working. I'm starting to think it might be a hardware issue with either the squirrel or PCMCIA slot.
