It all sounds plausible. I guess that if the holes taper (slightly) from top to bottom they would guide the base of the stone to the exact position. Wedges could be used to plumb up the uprights and then removed as needed to allow a small amount of lateral adjustment when the lintel is being fitted. I can't see any reason why a large stone should not behave in the same way as a scale model, so we ought to be able to evaluate the exact height/offset needed to hit the hole every time using a small block of stone/concrete (e.g. a kerb stone). Do you know what the dimensions of the trilithon uprights are and how deep will the holes need to be?