To me, removing them have sorted the timing issues for the most part. So far it has been running about 3-4 hours now and it hasn't even froze yet, which shows that it's unlikely and the computer is usable for the most part. While not a full fix itself since it's obvious that it is indeed more than removing a few capacitors, I am not going any further since my confidence in electronics only really goes so far. I'll leave that to Amigakit once it's needed.
However, a PSU-related issue would need to be sorted regardless simply because 1200 PSUs are not known to be particularly beefy. Even with the full timing fixes, there's no harm sorting out a new PSU to completely rule out any other issue that can cause freezes.