Even though a bent thread is ugly, the taper is the strength of the assembly, and the nut holds the flywheel firm onto it. I have seen plenty of cranks over the years with bent threads that still work fine. As long as the thread itself is ok and the nut is a nice firm fit on it, and there is no damage to the taper, it will be fine. i use a crank removing tool mostly, and I never hit the end of the crank if possible, or if i have to i press the crank out of the cases in a press. Worst case scenario if you have to hit the crank, use a copper hammer, and spin the nut on first till it is flush with the end of the crank. Always, always measure the crank width before splitting it, and always, always , check side clearance once the crank is reassembled and trued. I have had some where I have reassembled a crank to the width it was before it split it, and using the same width thrust washers, I have found the side clearance is too little. Most manafacturers will have the width of the crank listed in workshop manuals, or if not the correct side clearance.
