@drbytes,
Interesting that your other Amigas show some kind of reaction to the 3.1 roms you're having trouble with. It would not be a good idea to use roms meant for another Amiga in your 3000. There are differences, for a reason, and it may go beyond just SCSI not working right. If anybody in your area has a 3000 and is willing to help, maybe he or she could try your roms in their machine and see if it works and you could try theirs. Also, if anybody near you can loan you some older roms, such as 2.04 roms, to try those out and see what happens. If it works with those, then suspect a compatibility problem with your 3.1 roms.
I do recall instances where for whatever reason, a zorro card or upgrade chip would work okay on one Amiga but not on another that was apparently identical right down to the motherboard revisions.
Having the old bootroms that load kickstart from disk can cause lots of problems, as you probably already read. You tried disconnecting the harddrive and booting from a disk? The A3000 will sit there for a VERY long time with a blank screen while the harddrive times out. On mine, this sometimes takes up to two full minutes.
-David