The crash problem most likely came from the restart.fl file.

AFAIR crossfire is known for having problems after deactivating the mod. It was at least for 1.7 the case, not sure about 1.8.

Sometimes FLMM 1.4 or 1.5Beta can cause problems, so I guess the safest solution is to stick to 1.31. You can’t use* mods which are compressed by 7Zip (or was it just for the ultra compression).

You can’t “install” them to FLMM with double-click, but you can still extract them with winrar or 7-zip into your “mods” archive of FLMM and activate them then.

For the problems for the two mods I suggest you install FLMM 1.3 into a different directory.

If you have problems with Freelancer, try this:
Deactivate all mods.
Tools -> Restore backups

For SP you surely want to try out adoxa’s single-player console and maybe also FLHack - You need FL v 1.1 (it will still be shown ingame as v 1.0)

Also, I recommend that you make a backup copy of Freelancer after you installed it, if there are any problems with it (which can occur a lot with that game) you can simple copy your backup folder.