My goal is to get 3.9 installed so I can use a 80gb ide drive via Elbox fastata 4000.
You don't need OS 3.9 for this. The FastATA software in combination with a new file system like SFS is sufficient. OS 3.9 only makes it more complicated.
Also installing OS 3.9 on top of a customized 3.1 might be problematic, either. OS 3.9 assumes an unchanged installation. Any add-on to 3.1 might make 3.9 fail.
Bye,
Thomas
