No reason to drill the five holes early. Wait until you are ready to drill thru the weldment. Step up from #40 to #30 on up to the finish size. Here's my log entry on this from 11-29-2005:
Before drilling the bolt holes thru the 970 skin/lower longeron into the landing gear mount, I put a bolt in the top and bottom outboard gear mount to wing spar holes where the outboard 1/4" bolts thru the wing spar would be. This helped to make sure the gear was flush with the 904 bulkhead before drilling. Next I drilled the five hole each gear mount and put bolts in each hole. Cleaned out the shaving using my steel measure before putting in the bolts. Then on to the forward screws, two on each mount. The forward most hole is behind the 902 bulkhead so this presented a challenge. First I drilled the hole not behind the 902 bulkhead. From the outside I measured from the center of the hole to the bottom edge of the 970 skin, marked and drew a line parallel to the skin edge that distance from the skin edge. The holes are 1" from center to center, so I put a marked 1" forward of the hole. I drilled this with a 1/16" bit to make sure I rung the hole in the gear mount, then enlarged to #40, then #30, then #12. This worked well, or maybe I was just lucky. Once drilled, I countersunk and bolted in the screws on the right side.]
Hope this helps.