Wait, you said you "Low Level Formatted" the hard disk?

You're never supposed to do that w/ an IDE disk!  Although I'm no 
expert, I understood that if you do this, you destroy data that the 
disk uses to identify itself and its tracks to your computer (could be 
wrong here though).  (SCSI drives use a LLF to map out bad blocks - 
IDE drives are supposed to do this dynamically, and since the tracks 
and related disk data are set by the manufacturer, when you LLF an IDE 
disk, you corrupt or destroy information needed to safely operate the 
disk.  A LLF on an IDE disk can ruin the disk completely).

That would explain why even when you are booted from a different disk 
you can't use Starup Disk control panel - it checks for boot sectors 
on all your installed HDs, and if it finds something it doesn't like 
on your IDE disk, it might crap out and crash.

Out of curiousity, how did you manage to low level format an IDE disk 
anyway?  Disk Setup won't let you do that normally (it hasn't let you 
LLF an IDE disk for YEARS, since somewhere around System 7.5) - did 
you have your book in SCSI Disk Mode when you formatted the disK?

Peace,
Drew 
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