I cut the flanges as simple rectangles using a cutting wheel in my 4.5" angle grinder.

I used foil tape to template the heads. Then I used the template to locate the first hole, drilled it to 3/8".

I cut the heads off six bolts to use as locator studs. One I ground to a point in the drill, simulating a lathe, to use as a center punch.

I screwed a stud in the head in the first hole, and the center punch stud in the rear hole. Slid the flange over the locator stud, and smacked the flange with a hammer. This effectively marked the rear hole.

Using this method, I located and drilled each hole.

The flange was a tight fit over the studs, so I over drilled all holes by1/32". Now the flanges are a smooth fit over the studs.

I'll take them to school and cut the port holes on an end mill tomorrow.