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.
It is only because I wanted to skip mouse button check if the system was in MorphOS already since the same startup-sequence could be used for MorphOS and AmigaOS.
That is, booting to MorphOS requires resetting machine (done automatically by bootstrap) and re-executing startup-sequence again. Little bit like using softrom updates.