Swap the CIA's and see if the problem changes, can't hurt anything, however it's Paula that controls the disk drive.
You can boot from an external drive just fine depending on what version of Kickstart you have (select from the Early Startup screen) however most games or software that is hard coded for df0: won't work this way.
I believe there's a few different methods of rerouting df0: logic to an external drive, hardware devices, etc. Probably still cheaper to just try with a replacement drive first.
