Thanks SluckyD. After reading the ongoing debate about TESVSnip I've decided to hold off on using it until some of the kinks are worked out. It's way over my head so I'm not going to comment on any one side of the debate.

I appreciate your help nevertheless.
I have removed all LCTN records from my mod, both by taking them off of the cells and quest aliases one-by-one (only 2 cells were using the custom, non-vanilla location) and then setting the actual reference itself to be ignored in file details. Unfortunately users are still reporting CTDs with various mods. It seems most other house mods don't suffer from this issue so I'm wondering if I'm doing something horribly wrong here. Funnily enough the 2 mods I mentioned in the OP seem to work fine now, so perhaps my custom location broke them. Now it seems there's about 100 other mods that mine doesn't play nicely with so that's fun.
I don't have Update.esm as a dependency for my mod, could that be a problem? I'm not sure how to add it in, as I have a master file of my own. When I try to load Skyrim.esm, Update.esm and Nchuzzrezar.esm the CK scolds me for trying to load multiple esm files and doing it like that is the only way I know to add a dependency. Le sigh.
Here's a screenshot of the records included in my esp file: (not sure how helpful this is but it gives an idea of the extent of what my mod edits)
http://i.imgur.com/K3AIH.jpg
...and esm file:
http://i.imgur.com/g3adY.jpg
Once again, absolutely no vanilla resources were harmed in the making of this mod. The worst I did was disable some exterior trees that would have otherwise blocked up the courtyard. Any time I edited anything at all I created a custom version of it to toy with. No actual snipping occurred during the taking of these screenshots.
Anyone notice some glaring, conflict causing error? Some kind of record I should not mess with lest I make everyone's computer explode? Can you tell I'm frustrated? I think I'm going to give up on the whole thing soon.

Edit: Apparently I can't use BBCode to post the images... they aren't rickrolls I swear...