This really sounds like SCSI termination/power problem. If any of the chips (or the daughterboard, check it) is badly socketed, you either get a black screen or red one w/ daughterboard/memory/kickstart problems. So, check that you have terminator diodes in place on the motherboard. Also, add active terminator to the external connector, that should make the SCSI bus pretty much fail safe.
There are some SCSI bus signals near the battery, so you also might have cut traces. Check with multimeter, visual inspection is not enough. For me, the SCSI led is dead although I can not see any problems by eyesight only...
