Probably the best and easiest way if you happen to know the specs for the thread is to just run a tap and die through them to clean them up and bring them to spec. Unless you happen to have the right tools on hand or are good friends with a plumber or machinist or something who has them and will let you borrow/use them that’s probably too big on an investment in tooling to be worthwhile (probably looking at a couple hundred bucks.) Similarly if you have access to or know someone with a lathe they may be able to do it on their machine.

Other than that, you can try to clean them up manually with some sanding/needle files/being very careful with a Dremel. I’d try covering the threads with some sharpie or something similarly thin and can be worn off easily that’s not going to really affect the dimensions and screwing it together and jiggling it around a bit to see where things are rubbing to know where to focus your sanding

You could also try heating up the female threads a bit to try to soften them up then forcing the male half into it and see if you can reshape them a bit that way. Heat gun is probably ideal, a hair dryer might do the trick, or a torch or lighter if you’re very careful.

As far as adjusting your machine or the model to make it work, I can’t really be much help

My experience with threads is to use offsets when modeling in F360- usually 0.1-0.2mm. That’s not an option for stl parts.

But also…that thing scares me. That I know what it is and what it’s for scares me even more. 🤪☕️