Its not clear to me if you've installed the

- original CPU

- original hard drive or small capacity SCSI on the SCSI-1 chain

in the bare system.

I'm also not clear if you've actually tried to boot from the internal CD-ROM drive using an OS 9 CD-ROM

I'm also trying to remember if your Mac Radeon card required any extensions to be installed

Have you tried SCSI disk mode from your 3400 to the 9600?

This is making me want to pull out my 9600