Are the post holes drilled all the way thru as well?
I would try and make a paper layout ..... put a piece of paper on it then rub with a pencil to trace around the holes ... then punch them out with a hole punch the right size ... from there lay the paper on the slide.
Or make some small posts to fit in each hole with a point on them in the center of the post, insert the posts into the hole, .... dykem the slide.... use the point of the posts to make the location for the holes in the dykem... then put the slide back in the mill and mill the holes big enough to tap.
No sir the post only go up about 1/8" and stop. They are just studs helping secure the sight. Thanks for the suggestions both seem reasonable options if I can't get a system that is more accurate.