I use the tool that either Great Planes or Top Flite makes that has a centering cone and a pilot drill for marking center. i position the engine and mark one hole. I drill that hole and put a bolt in it and secure with a nut, or use a blind nut. Then I recheck engine position and do another hole, catty-corner on the other side of the engine, drill that hole and secure again. Then I mark the last two holes, drill those and there you have it. I don't recall ever having any problems with this method.
Jim Lee makes drill jig templates for the popular engines. If you use only one or two brands or styles of engines, these are well worth the cost of having them in your tool chest.
Type at you later,
Dan McEntee