Interesting project ahead of you. It must have been a killer machine in the days with 16 Mb fast.
I'd go for the 3.1 chips, just because it's... so much easier than the hazzle with softkicking. And sooner or later you probably want to upgrade the CPU anyway.
I would also check out the Buster chip, get a rev 11 of eBay. Same thing with the WD SCSI chip, it looks like you have rev 4, I believe rev 8 is the latest to look for.