Regarding the user side of the problem, you might(!) be able to work around the crash by merging nested if-conditions into and-expressions if they have no elif/else. That's also why the split into multiple files doesn't help, it's the depth of the nesting and the overall code complexity that strike here, not the total length of the program.

Side note: just for fun, I compiled your file with Cython. It took a few minutes and then generated a 1.1 GB C file :D - hadn't seen it do that before. That's 31MB xz compressed. I was sure it would crash my C compiler if I tried to compile that, but since processing time and renewable energy are cheap these days, I gave it a try. Now "gcc -O3" is still working on it after 7 hours, currently using some 8.5 GB of RAM. It's probably worth first recompiling gcc itself with proper C compiler flags next time...