Could be a problem with Gary, as this device does a lot of misc system control functions.
Were the new parts you fitted definately in working condition?
It would also be worth checking if termination power is being supplied to the internal/external SCSI ports. This comes from diode D800 (between the ext floppy and parallel port). With SCSI devices connected to the motherboard controller, check for approx 5V on the cathode of D800 with the system running. If there is no power (probably due to the diode being open circuit) then replace it with any common power diode such as a 1N4004.
Also make sure the boot device has a SCSI ID of 0, I've found this can sometimes help, as it's the first ID to be polled on power up.
Replace or check that the internal 50 way IDC ribbon cable is not dodgy. The connectors can go intermittent when you least expect it.
If you need details of the SCSI controller, you can get schematics and the full service manual from my website:
http://amiga.serveftp.netAnthony.
