Hard to explain, but here goes...

Use a magnet to hold the flat of the cotter. Clamp the cotter, still held by the magnet, into a vise. Before snugging the vise, ensure that there are two spacers, one each side of the cotter and flat to the top of the vice jaws. The shims should be roughly ten thousands of an inch thick.

Once clamped in the vice, remove the magnet and the shims. Now the flat of the cotter pin will be sitting, parallel to the top of the vice jaws and ten thousands of an inch high. Simple file the cotter flat even with the vice jaws and, voila, control angle and amount of cut (removed portion) completed. NOTE: Your file will do little damage to the hardened vice jaws and you will know when you are done filing.

Try the cotter, and, if necessary, repeat the above procedure. You will end up with two identical angles and parallel crank arms, with the cotters properly fitted. Now, press them into place with that fancy press, or build up what I use for next to nada...