According to my A4000T manual, A4000T Motherboard Jumper section: (Excuse the bad ASCII picture)
CLK90 Clock Source
J100: 1-2 closed - Internal (68030) <[··]o
J100: 2-3 closed - External (68040)
CPU Clock Source
J104: 1-2 closed - Internal (68030) <[··]o
J104: 2-3 closed - External (68040)
These would be located near the CPU slot. I think they should be set to 2-3 (away from the end with the triangle)
SCSI Dip Switches (all set to OFF by default)
SCSI Address
Tabs 1,2,3
SCSI Fast Bus
Tab 4: Turn on to disable SCSI fast bus
Short/Long Spinup
Tab 5: Turn on for long spin-up
Synchronous Mode
Tab 6: Turn on to disable synchronous mode
External SCSI Termination
Tab 7: Turn on if you have external devices
Logical Unit Enable
Tab 8: Turn on to enable all LUNs to be recognized
I have had many problems with my A4000T, so I think I can help a little. :-) I've put the ribbon cables for the port module on wrong, and had similar problems where the mouse would not move sideways.
As for problems with stabilty, try laying the A4000T on it's side (like a desktop). Might be that the accelerator card is not sitting right in the cpu slot. You might have to put spacers under the board to keep it sitting right.
