The floppy drive issues is probably the bourns filter needs to be replaced.

but could also be some dead traces to/fro swim same as the with the SCSI issues

when you removed all the caps, did you wash the board in hot soapy water scrubbing it well,  then giving a hot water rinse,

then a good blast off with an air compressor,   Chances are you still have cap goo causing you stability issues.