If it were me, I'd drill the bolt out (carefully) and re-tap with a slightly larger bolt. You'll probably have to enlarge the holes in the gudgeons (or tap them out too).

If that didnt work, I'd put in two port access covers and go back to the original size bolts and add fender washers and nuts on the inside. A little silicone in the holes before assembly will keep it waterproof.

Drilling holes in a new location sounds like a bad idea, lots of opportunity to for mis-alignment.

Bill