All - thanks very much for this advice. We decided to make a fixture plate which will hold a drill bushing, like Gordon suggested. We'll tack weld the fixture plate to one of the flanges, and then use a mag drill to enlarge the holes. We'll then use a long pilot adjustable reamer (
https://www.mcmaster.com/adjustable-reamers/straight-blade-adjustable-size-reamers-8/) to get the holes into alignment and tolerance. Then add the bushings.
To answer some of the questions above:
1) The two bolt holes are 7" apart.
2) We need a tight fit on the bolt (hence, the 0.002" tolerance). The old holes were loose, and the bolt pounded them into an oval shape.
3) No, this is not a dirt bike.

It's a piece of ag/construction equipment.
Thank you again!