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The critical measurements are the dowel pin locations and the crankshaft center...and they aren't nearest-thousandth critical 'cause there's some flex in the transmission input shaft. Once you have the engine and bell housing dowel pin locations in the right spots (and put dowels in them), you can use existing holes as your guides. For the through holes, mark 'em though the holes--use transfer punches if you've got a set (or if HF is running a special). For the threaded holes, I've used grub screws with an internal hex (Allan head) and cut off short pieces of the appropriate allan wrench, sharpen them on one end, and put the other end in the grub screws. Then put the adapter in place (located with the dowel pins) and tap it with a soft hammer; the pointy things you put in the grub screws will mark your mounting holes.
Also there are places that measure this sort of thing for a living. Call a local high end machine shop and ask if they have the equipment in house, or if they can recommend anyone who can do it for you. If you bring in two <very clean> bell housings (one to fit the engine and one to fit the transmission) and a hundred bucks you should get all the info you need.
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