I think I managed to get the hard drive set back up correctly.  It was put into storage in the same condition that it was when working, so it doesn't make sense the settings would have been changed.  It's unfortunate I didn't know about needing to smack the drive before I went to all the trouble to take the whole enclosure apart. 

I'm going to crack open the Mac's case tomorrow and assess the damage.  There was a whole lot of smoke and it didn't really smell like burning dust (strong "electrical" smell).  There was so much smoke that under normal circumstances I would expect the whole machine to be dead.  Maybe it could be from leaking capacitors, but I'm wondering if the SCSI control chip didn't get fried or partially fried.  Anyway, there's one way to find out. 

I'm hoping the worst case scenario is needing to replace the logic board.