Looks like I fixed my problem of vehicles phase 3 & 4 weapons not spawning when producing them. I deleted my C:\Users\Username\AppData\Roaming\Goldhawk Interactive\Xenonauts\internal file as you recommended in your main post, and I properly applied the hotfixes in the 4. Known Bug by putting them into the X-Division 0.99 Beta mod folder in the assets folder. Smooth sailing so far.
In my broken save, I noticed that whenever an alien threw an advanced alien neutron grenade, it would crash my game. I'll see if I run into it again with my improved patched version.