Moto,
Have you found out the 1230scsi.device version (using shell> version 1230scsi.device) to make sure yours IS the later version which does not need to be patched using the softscsi tool you mentioned earlier in the thread?
If you have the space, why not do a basic installation of oS3.0 on another partition of the SCSI hard drive.
Since setpatch is much simpler (does it even exist with 3.0? can't remember) the amiga should boot fine straight off the scsi.
- If it works - you know setpatch form 3.9 is patching something preventing you booting.
- If it does not work you know that the scsi controller (or the cable) is not correct. Since you are having problems with the CD rom aswell it may be a scsi controller problem.
Weird that it would work with IDE connected though...