Talk to Chuck at Best Machine about lifter bore positioning. They do it on their Rottler and get it correct. From what I understand the lifter bore positioning from Indy was so bad that Best started to buy the blocks unmachined and they finish them at their shop.

So it doesn't take a huge machine, it just takes a good machinist who pays attention to the setup and gets the block properly fixtured and indexed. Sadly it appears that lots of people have problems doing this. I've heard that Indy, the old KB and even the new block that Muscle Motors was selling all have had lifter bore issues.