So, I downloaded http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=7329 race. Then I tried to join the Thieves' Guild. Every time I ask about "join the Thieves' Guild" topic, they say "want to, or want to hear the rules?" and I click yes to join, it just gives me the prompt again, over and over, asking me if I want to join or hear the rules. Only way to get out of it is to hear the rules and then say "no, nevermind".

I can only assume that it's because of the new race. Never had anything like this happen before, and none of my mods touch the Thieves' Guild, so it wouldn't be that. Anybody else have this, or know how to fix it?

Do you have Tamriel Rebuilt map 1 active by any chance? It is a known bug with it's older version - the newer one, http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=7040 has the issue resolved.

Ugh.. that cause many facepalms on my part. But yeah, likely the problem, right there.

Ah, yeah, I did download them separately this time. That might explain the missing cell error message having to do with a TR cell that I didn't get before, too. Thanks.

Sooo... I haven't gotten far enough to see if this is the case for everything yet (in this faction, the others work fine) but so far I've killed Toris Saren and Odaishah Yasalmibaal and neither one gives me the journal entry after I kill them. It worked fine for Feruren Oran. I can enter the journal entry with my console and continue fine. I've gotten the correct TR and solved the issue from my OP, but now this is happening. Related?

Not related to TR. (at least no one has ever reported this with the Morag Tong and TR before)
If you want any real help, please start by posting your Load Order.
And I suggest running it through http://code.google.com/p/mlox/wiki/Mlox, too.

Also, note that you won't get a Journal update if you haven't been given the quest yet. (just in case you're killing them before you have to)

I don't use Wrye Mash or anything, so I'll just list the order that they're listed in Data Files when I've got the MW loading screen up. I have the quest to kill them, got the writs and everything, but when I kill them I don't get the entry saying I've done so. As such, when I try to turn them in I just get Eno Hlaalu saying "I already gave you the writ for him."

Morrowind.esm
Tribunal.esm
Bloodmoon.esm
Morrowind Patch v1.6.4.esm
GOTYScriptTidy.esm
Better Heads Tribunal addon.esm
Better Heads Bloodmoon addon.esm
Better Heads.esm
Book Rotate.esm
GDR_MasterFile.esm
MCA.esm
TR_Data.esm
TR_Map1.esm
TR_Map2.esm
Rise of House Telvanni.esm
Ring Texture Fix.esp
Clean Weapon Sheaths Ultimate.esp
Better Bodies.esp
MWE_Writing.esp
MWE_Base.esp
Book Rotate - Tribunal v5.3.esp
Book Rotate - Bloodmoon v5.3.esp
Galsiahs Character Development.esp
GCD StartScript for Trib or Bloodmoon.esp
GCD Over 60 level speedup.esp
GCD Restore Potions Fix.esp
MCA - Guards Patch.esp
MCA Names 5.2.esp
BB Dark Brotherhood by Westly.esp
Real_Katana_Lite.esp
DN_GDRv1.esp
BUUG Alchemy- Bloodmoon.esp
BUUG Alchemy- Tribunal.esp
Xenn's Shadowscales.ESP
Pursuit Enhanced.esp
UniqueFinery.esp
Better Skulls.esp
Census and Excise Office.esp