Did you take a look to see if the jumpers between the cdrom and zip drive aren't the same?
Did you double-check that the ribbon cables are properly connected on both drives and Amiga interface?
Do you have an extra ribbon cable to test?
Did you try at least one of each to see if it boots up?
Did you reverse the jumper settings on both drives to see if that helps?
Can you test each drive on another Amiga with IDE to see if it isn't malfunctioning?
See if these process-of-elimination steps help. If not you may have to revert to the older filesystem if a reinstall failed. And, just out of curiosity, which filesystem did you use before using 3.9's filesystem?
