Semi unit gearbox replacement

[Jackson]

When I dismantled my gearbox and engine ('53 Flash) there were only three screws (one missing)holding the gearbox to the engine. Looking at the parts list this shows two studs (lower) and two screws (upper).
Now I come to put it back together I am faced with two problems. Firstly , if I put studs in the bottom two holes as per the parts list I can't get the gearbox back on due to the drive shaft getting in the way.
I can use screws as the lower fastenings to get round this problem, but both the upper holes don't seem to want to take 3/8 Whitworth screws. One of the holes looks like its threads are a bit mangled and I'd thought of cleaning them up with a tap - any reason why I shouldn't?
The screws I've got from Draganfly are a bit of a surprise as well. They are the correct diameter but the heads seem small (my 5/16 spanner fits them), but my thread gauge says 16 tpi 3/8 and I measure the outer thread diameter at about 0.298.
Any thoughts would be gratefully appreciated.
I'm currently thinking of running a 3/8 tap into both the upper holes.

[Jackson]

Sorted now. Holes tapped out larger. If that doesn't  work longer term will helicoil
them.