Being the simpleton I am, I forgot to update tesvedit, so my mods are now all properly cleaned. Cut back a bit on the mods too, uninstalled a couple of hair packs and equipment mods I wasn't using at all. Most of the boss errors are gone as well, after much uninstalling, updating and reinstalling.
However, all of that wasn't enough, the CTDs were still occurring.
I figured one of the unrecognized mods were to blame, since everything else has played nicely before, and it turns out that the SG Skin Textures (ECEESCv.esp) were causing quite a bit of fuss. Uninstalled, and everything works fine. For now, at least.
Thanks for the assistance. I should really stop downloading mods on a whim D;
EDIT: Okay, maybe I'm not quite done yet. Getting some script lag(? Things are acting delayed, like sounds, animations, and my movement) now, but it could be my computer acting up.