Ok, Dumb question but you do have SFS file system files installed on the new SCSI's system (boot) partition and are using the SCSI drives HDToolbox to set up your new drive? Because if its still set up to look at the IDE drives system partition to find the SFS files it will not work.
The best thing to do is copy over all of the IDE's system partition over to the new SCSI system partition. Make sure you have the SCSI drivers installed as well on the new SCSI drive.