Are you saying if you just plug the floppy drive in without a disk, the ? never appears? Same for SCSI?
If that's the case, I'd check for damage around Grand Central (343S1125). Or in the traces that connect it to Bandit (343S1120). Grand Central is a PCI device. SCSI and floppy control are both through Grand Central. SCSI is further controlled by CUDA, but the floppy drive is controlled by a different chip. So the thing they have in common is Grand Central and everything upstream from there.
But video is working, so the upstream stuff -- PCI and points north -- must be working. So I would think Grand Central is the place to start.
BTW, Bandit is the PCI controller. Oh, and don't neglect the PCI Arbiter chip. Everyone focuses on Bandit as a "PCI Controller" or "PCI Bridge" but it is not complete without an arbiter chip. Can't remember hte part number on the Arbiter. It's a little square 28 pin PLCC chip. Something like 341S0181 or some such. It'll be near the PCI slots and there are two of them -- one for each bus.
Is you video card in the upper or lower three PCI slots? If the lower, then video working, doesn't mean that Grand Central's Bandit is working. Grand Central is on the upper PCI bus. Slots 1, 2, 3.