I have an Amiga 3000T-040 comuter (extremely rare version of the Amiga 3000T). Anyway, the computer works fine with the original Commodore 040 board, but, will not work with the Cyberstorm MK II 060 board. I read that there is a missing signal on the Amiga 3000's processor slot. Could this be the problem? I pulled the Cyberstorm MK II 060 board out of a working Amiga 4000 Toaster system, it had a SCSI module plugged in. I removed it and put it back into its original box for safe keeping ( the A3000T already has SCSI ).
Did you install the proper 68040,68040 dummy,and 68060 libs correctly?
The A3000D/T were missing the INT2 interrupt line,i have never tried to run a CSMKII without the line,so i can't say for sure if that's your trouble.At a minimum,you need int2 to use the scsi.C= left this line off the A3000 cpu slot(dave haynie talks about it).
The 3000t jumpers are super picky and just 1 wrong jumper can cause a no boot situation,i urge you to review all of them before giving up.I have heard there are cases that the onboard 3000 scsi and the MKII scsi don't get along but this could of been termination issues.
Btw,Phase 5 made some pretty good stuff,they at least tried to push the envelope a bit.Of course some CSMKIII/PPC boards had 060 socket troubles.