Occasionally textures + meshes will be missing, becoming giant red exclamation marks. Icons in my pipboy turn pink, and my crosshair turns in to a red square. After this, I'm unable to open the menu and when I rejoin the save file it happened in is gone completely. I don't think it's a problem with my load order- I have that managed.

Bad things happen if you go over the mod limit, somewhere around 130-ish. That's what it sounds like at least.

sounds you reach the modlimit or you have missing files or mods that conflicts

Depending on the mods you've installed, it could also be possible that the system is out of memory - or at least thinks it is, meaning do you have the 4GB patch installed?
You could also ajust the following lines in the Fallout.ini and FalloutPrefs.ini (both to befound in My Documents/My Games...):

Code:

uInterior Cell Buffer=

Code:

uExterior Cell Buffer=

Code:

iPreloadSizeLimit=