I made a few drilling jigs out of scrap hardwood on a drill press.
Ran the wood through a planer both sides to make sure they were very square. Then used a drill press and made all the reqular size hols through the board.
1/4, 5/16, 3/8, 1/2, 5/8, 3/4, 7/8, and 1 "
Boards were:
2 x 4
4 x4
4 x 6
Basically free if you have the tools and will keep you drill aligned and won't wander.
Start the hole with the deepest the drill will fit. Then switch to the thinner boards as the hole progresses. Your holes will be true.
Another super cool trick (not as cool as Bud's trick but nonetheless) Get some high quality polished non-threaded hardened pins of various sizes. Grease em up, tape the underside, and then you can whack- em out after the poured epoxy cures for a perfect fit. This if you need very waterproof precise holes.
Lots of variable methods using the same principles.