Only other thing I can think of would be to zap the pram and see if that clears up the scsi issue...if you can boot it. Or, try pressing and holding the reset button on the back for a minute or so.

Not sure where the scsi controller is located on the mainboard...the only scsi devices I ever used with my 5300s was an external CD drive, and that always worked OK.

Cheapest option may just be to pick up another 5300 on the 'bay? I imagine mainboards are scarce now.