3/8" rat tail file slipped through holes, with vise grips clamped at 90 degrees in the middle to serve as a handle. File to fit bolt. Cut file off if it's too long. A 1/2" rat tail file cut off, flats ground, and turned Left handed will also work. This prevents the file from being pulled into the hole and wedging. Turning in this manner will allow it to cut, while constantly pushing itself out of the hole and clearing chips. A rat tail file with the tang ground off and chucked in a drill run in REVERSE makes a wonderful sheet metal reamer. Cuts smooth as butter. I have reamed mis-aligned 3/8" holes through 3" diameter steel male-female shaft assemblies like this, for shear pins.
RJ