I don't really understand running MorphOS on an Amiga rather than a PegII, so please somebody let me know if I'm wrong here :-)
I don't see why you need to check the processor being used in order to select the OS if there is a Morphos "startup script". Why can't you use checklmb in the AmigaOS startup-sequence, and in the IF WARN statement following it, just enter the execute command for the MorphOS startup script. That way the script will be run if the LMB is pressed when you boot, and then MorphOS will start.
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moto