Patched!
For some reason XMLpad wasn’t saving the file the same way; and notepad wouldn’t let me save any changes to the beam weapon mod. It said access denied. Later after messing around with it I realized that for whatever reason it wasn’t recognizing me as administrator. So I moved the script onto the desktop; edited it there with notepad, and moved it back into the mod folder.
I’m currently running around with 5 advanced beam weapons on a defender fighter. lol. It keeps me laughing. I just look at something and its gone.
As for the other crap; for some reason the mod manager seems to (mostly) be behaving itself. The speed mod is still off; I doubled the cruise speed to 600 but the gauge is still readin 300 even though I can tell by how quickly I’m closing range I’m going 600. Whatever. Everything works now!