I consider using a die to be last resort. A fine triangular file (for the obvious bad spots), a metric thread file, a smallish hammer, and a regular nut of right diameter and pitch is my preferred "tools". First clean up the worst with the triangular file, then the thread file. Oil the threads lightly, and screw on the nut BY HAND, until feeling resistance. Then tap the nut with the hammer, from all directions. This will flatten any high spots without removing material. Then screw the nut a little bit further, and tap again. This works. If you dont believe me, take a random bolt from your "miscellaneous box", and hammer the threads flat in a couple of spots, bad enough to stop the nut. Then oil it, hit it with the hammer as described, ren the nut a bit further, hit it again, and so on. Before you know it, the nut will screw on like new.
For wheel axles and swing arm pivot bolts, you don't even need a hammer. Just something a bit substantial, like a vise or anvil, or some other heavy and solid steel object. Just hold the axle as a hammer, and tap the nut against your "anvil" of choice, on all 6 flats, then screw it a bit further, until next rough spot, and repeat.
My mentor at the shipyard where I did my apprenticeship in the 80s taught me this trick. He was already in his 60s, and absolutely refused to fit any nut or bolt that wouldn't thread on all the way just by hand. And he hated Loctite, Nyloc nuts, and stainless fasteners with a passion
RIP Einar.