Hi X-Ray,
first of all:
CSMK2> INT CLOCK
CSMK3-PPC> EXT CLOCK
then . . take a look at the CSPPC Bios config (ESC during the boot) and check if something is screwedup (there is a switch to enable-disable the internal SCSI A4KTower controller)
Try to disable MapRom and play with the RAM configuration too (you can't damage anything)
Good luck :-)
EDIT- check to have the right 040 and/or 060 libs
If you have AOS3.9 with BB2 and a 060, you can install only the 68060.library.
Or you will need, all the 4 libraries with the 040 dummy one.
68040.library
68040new.library
68040old.library
68060.library