From memory, I used quite tight clearances. Like 0.1 - 0.2mm
Most of the bits that needed to fit together would have been possible for me to simply file by hand if something didn’t quite fit. Luckily, everything fit nicely.
I just left anything that needed to be threaded as the nominal drill size, as if I was going to run a tap through. And during the ordering process, I specified where I wanted tapped holes. I did not print anything with an external thread.
I think the general recommendation is not to print threads.
Lots of good info in this thread: