Having just gone through this process in my A1200 (similar setup - 3.1 ROMs, 3.9 CD, 60GB HD and IDE CD-ROM on internal port). My 3.9 boot disk was made on another Amiga, but the CD drive worked fine on it. If you put the IDE-Fix files on a floppy and use it to examine the devices to find the CD drive, that'll tell you if it's detectable (maybe it just doesn't play nice with that hard drive). You might have to boot the emergency floppy with no startup-sequence and use the shell to get there...
If you can boot to 3.1 and install IDE-Fix from there, you should be able to use the big drive in 3.1 provided you use a 64-bit filesystem as well (SFS for example). Also be very careful with Shapeshifter, as Thomas pointed out, and don't full format any of the partitions...
