Glad your 1000 is working again! I totally hear what you're saying about not fixing it if it's not broken...I recently bent (but thankfully didn't break) a pin on the 68000 on one of my A500s, after swapping it while troubleshooting another machine. I'd broken the socket while prising the chip out, glued it back together, and a tiny amount of glue must have wicked into the wiping contacts on one pin. A simple desoldering job can get unpleasant if things don't go well!
The SMD capacitors in the A600/1200/4000 are notorious, but I haven't seen too many issues with caps on the 1980s Amigas. Do you have (access to) an ESR meter? I believe those can generally give indicative results with the caps in-circuit.
