Excure my terminology ignorance,but are you talking the transom holes to bolt your engine on?
I was told a while ago that they should be pretty standard after about 1990-ish, and so far I have swapped or helped in a few swaps where it weas literally a case of bolting the new engine in where the old one sat. Certainly works in the "mid power" range.
Fainling that, could you make a template from cardboard using the engine? Alternatively if you have a crane, old the engine, carefully mark the positions, themn crane the engine out the way while you drill?