what procedure did you use NH? sounds like a tricky one.
One possible solution is to cut a block with an angled side to match the carriage sides, so that when placed against the timbers the sides of the blocks would be parallel (I don't know how clear my description is?) These blocks could be held in place opposite each other, and would give you parallel reference faces for the purposes of marking and drilling. Then when you do drill, just go through both the block and the frame.