As I understand it:

SCSI ID 0 is, by definition, the boot drive during startup and this is set up in ROM . . .

. . . this can be overridden when the PRAM is read during the boot process . . . OOPSIE . . .

Du-oh! :I My bad . . . try zapping the PRAM as your first troubleshooting step. IMADOPE! :

After that, if needs be, swap IDs between your external SCSI FLASH Drive (if possible) and the borked Internal HDD.