Hi,
I'm working on a Classic board that does the exact same thing. It will boot from a floppy but takes a very long time, probably around 5 or more minutes to boot to the desktop. It boots fine from a good hard drive and passes all logic board test on the Snooper v2.0 test utility. If I boot from the hard drive, a floppy won't mount on the desktop. Have you made any progress with your board?
I've successfully recapped and repaired well over 50 9" Macs and have a dedicated test jig for the Classic and Classic II logic and analog boards. This board has been cleaned and recapped and my test setup works perfectly with a good logic board and my analog board voltages are spot on.