I've been trying to figure out how to remove the three Main Quest scripts from Ald-Vendras v3.1, but I haven't had any luck in doing so. I've looked into the CS, and was completely lost, and Export/Import Scripts through Wrye Mash didn't seem to change the existing scripts to the edited import. Could someone please let me know how to do so?

You want to completely remove these scripts form the mod? Just grab an editor like TESAME (TES Advaned Mod Editor) or EE (Enchanted Editor) and delete these records.

And now I feel silly for not trying that first. That was incredibly easy. Thanks for your help!