It is true that the last batch of 330uF caps are a little too large. We had to purchase these because of the worldwide shortage on the usual kind. It is not an electronic issue at all, actually the larger caps life span is better. Just arrange them the best as you can.
the 1000uF caps are very high, and touch the closing plate
No problem, the case is totally disconnected from the active circuits.
in Eurorack kits, there's this repeated rule of *never* soldering a front panel component
You are correct, the mechanical tolerances on both the plate and PCB are really tight.