Hiya,
As Rebel has pointed out, 3.9 really needs a bit more CPU and FASTRAM to get the most out of it so if you're going to stick with that card you're better off with 3.1.
If you did want to run 3.9 then I'd recommend one of the new ACA 030's.
You should also look at getting a CF transfer kit and have a good look at
Classic Workbench and
WHDLOAD