I take it you mean align bore it as it wouldn't make a difference in boring the cylinders. Back when we had piles of main caps we would try caps till when one was torqued down it would not catch your finger nail at the parting line. This would usually be close enough to clean up after boring/honing. If the cap is centered front to back then you could fly cut a new bearing lock notch on the opposite side and leave it backward. A really talented machinist could measure what profile was needed in the cap, bolt two caps together with each cap surfaced with an offset so that after honing one would have the the profile needed. Look for a machinist at least in his 70's for something like this. Now the young computer guys could slap some stock up in a 5 axis mill and make one accurate to 4 decimal places but the set up cost would be way more than everything spent on the whole project.
