Yes, I have 3.1 roms (KS ver. 40.68) and 16mb of ZIP's, and all of the custom chips have been upgraded including the WD-08.
Have the DMAC and Ramsey been upgraded also? Which 040 accelerator do you have? I have had random checksum errors on the SCSI bus with these chips and some accelerators. If I remember correctly, replacing the old DMAC only solved the problem despite the rumor that the new Ramsey and DMAC should be upgraded together. The new Buster and SCSI chip are good upgrades in my experience.
The 68040.library could be the other problem. You could try to remove the 040 accelerator (with needed jumper changes too). I bet the SCSI errors will go away and this will narrow the problem down. I very much doubt that the SCSI maxtransfer or mask are your problems as the 3000 is not picky about them. The 3000 SCSI is usually not picky about termination as long as 1 end of the SCSI bus is terminated (worth checking though). The reversed diodes on the earliest 3000 motherboards can cause problems.
