Reason for your problems is that the design & construction of the fixture is flawed in a number of respects.
Masthead sheaves are safety-critical. Using only two self-tappers to retain each sheave pin was a very poor choice.
Welding shaped retaining plates to pins is unnecessarily expensive, requires a different size for each mast section and is guaranteed to make them difficult to remove.
I'd have used a single
pin right through the mast so it could be driven out if it seized. I'd have used separate, larger cover/retaining plates with 4 fixings.
If the only option was to use individual sheave pins - drill & tap the ends for removal
with a slide hammer and again use separate cover/retaining plates.
To align sheave box cheeks precisely perpendicular to a pre-drilled hole through the mast is not difficult - it's only necessary to use a pin with large push-fit spacers as an assembly jig to align and weld the cheeks to the mast.
Do the screw holes in the new pin plates even line up with those in your mast? If not the screw holes will be weakened. If they do line up I'll be surprised - but it's still a ridiculous arrangement.
In your situation I would definitely not try to correct the holes in the mast.
Difficulty of making the holes perpendicular to the sheave cheeks without some trial and error must be obvious surely?
Looser holes places more reliance on those two screws.
Filing the cheek to avoid further wear to the cheek seems - odd.
Unclear what anyone thinks the downside to reaming the sheave a few thou might be?