Perhaps it can be done via CD some way without having to take out the CF card?
That cd drive is a 2x, so things will go fairly slow if you're planning on writing a lot of data. If you have a flash reader on a PC, I'd recommend doing all your file transfers there first.
I also had a problem getting OS3.9 to recognize the cd device properly. I had to use a custom cd.device, and even after that, drag'n'drop from workbench wouldn't work (other programs and command line could access the drive fine though). I'm curious if you've seen the same problem on your setup.