Update:
It starts up now... yay!
I found out that it was because I disabled this line in my main script: #include <mtlFX.c>

I don't know why I had it disabled. It did not cause any problems when running through WED. I wish I understood why this happens. It might help a lot.

It still crashes when loading a new level. But I think I can figure it out from here.

Some things I'm going to do from now on:
1. Always have a working version of the game saved separately, to fall back on.
2. For any new code, always test in published version before moving on to something new.
3. When testing published version, always check all the different actions and level loading/saving etc...

I'm still open to advice about preventing this sort of problem in the future. I figure it's good to keep track of these things here, in case other users encounter the same problems.