The holes in my frame are also 3/8", and fairly sure were that since I've had it since ~ '77, but I think all the boxes that I have are 5/16" mount holes, except the two that I've used and drilled and re-tapped to 3/8" 'cos the threads were shot (actually I think the one in use was already 3/8"- but shot, and I've used helicoils).
I ordered a bunch of bits from Lightning Spares, and in the 'Frame -Fastenings' packet were two 5/16" bolts that I've never used.
Also, the bottom gearbox lugs were both fairly hammered from (everything) being loose and bouncing around. To remedy this, I filed 'em flat and square and have packed it up with a couple of stainless washers with the intention of one day making a single piece two-hole shim to do same.
Hope that's a bit helpful.