Here's my mod list. I'd post it according to load order, but I can't figure out how to make Wrye Mash do that.
GameFile0=Bloodmoon.esm
GameFile1=Book Rotate.esm
GameFile2=H.E.L.L.U.V.A._Merchant_Containers.esm
GameFile3=Hilgya the Seamstress.esm
GameFile4=MW_Children_1_0.esm
GameFile5=MetalQueenBoutique.esm
GameFile6=Morrowind Comes Alive.esm
GameFile7=Morrowind Patch v1.6.4.esm
GameFile8=Morrowind.esm
GameFile9=Texture Fix - Bloodmoon 1.1.esm
GameFile10=Texture Fix 1.8.esm
GameFile11=Tribunal.esm
GameFile12=AOF_Undies.esp
GameFile13=AV_fem_armor_Trib.esp
GameFile14=AV_fem_shirts.esp
GameFile15=AV_female_armor.esp
GameFile16=Acheron's Camping Gear 2.esp
GameFile17=Akaviri Seconds.esp
GameFile18=Alakazar's Lamp.esp
GameFile19=Ald Velothi - Khuul Transport.esp
GameFile20=Alenne's Clothing.esp
GameFile21=Almilia's daughters 3.2.esp
GameFile22=Animated Morrowind 1.0.esp
GameFile23=Animated Soulgems.esp
GameFile24=Arkeylan Armor Collection.esp
GameFile25=BB Dark Brotherhood by Westly.esp
GameFile26=BB2_Silk_Dresses.esp
GameFile27=BB_Clothiers_of_Vvardenfell_v1.1.esp
GameFile28=BEER! with MCA.esp
GameFile29=BLLDV_ALL.esp
GameFile30=BadKarma's Anjurin Chest.esp
GameFile31=BadKarma's and Leeloo's Serenity V2.0.esp
GameFile32=Beds4Rent.esp
GameFile33=Better Bodies.esp
GameFile34=Better Clothes Beta_1.4.esp
GameFile35=Better Snow Prince.ESP
GameFile36=BetterBooks_AlchFormfix.esp
GameFile37=Blademaster Armor.esp
GameFile38=Book Rotate - Bloodmoon v5.3.esp
GameFile39=Book Rotate - Tribunal v5.3.esp
GameFile40=Brittlewind fix.esp
GameFile41=BuyableGhorakManorF.esp
GameFile42=CB's Gold+.esp
GameFile43=Cali's Clothing v1.2.esp
GameFile44=Cali_Dryad_Robes.esp
GameFile45=Cali_StarstoneOutpost.esp
GameFile46=Captain Jack Sparrow.esp
GameFile47=Cenobite's sixy Armor Collection.esp
GameFile48=Clean BadKarma Clothing Vendor.esp
GameFile49=Clean Caius Romance.ESP
GameFile50=Clean Elynda'sWinterWear.esp
GameFile51=Clean TF_bedreplacer_v1_MW_BM.esp
GameFile52=Clean TG's Nord Ceremonial Armor V1.esp
GameFile53=Clean To Serve Sithis_.esp
GameFile54=CleanBitterCoastSounds.esp
GameFile55=CleanMasterIndex.esp
GameFile56=Clean_Xia_Silk_Dragon_Imports_1.0.esp
GameFile57=Cleaned_Pearl_Palace_v1.esp
GameFile58=ComprehensiveChargen.esp
GameFile59=Creature Additon and Fix Mods.esp
GameFile60=Creatures.esp
GameFile61=Daedric Pants.esp
GameFile62=Dianne's Complete Tavern Time.esp
GameFile63=Disturb_the_dead.esp
GameFile64=Divine Domina Complete.esp
GameFile65=Dread Knight Gear.esp
GameFile66=EbnhrtFrtGrv_V1.5.esp
GameFile67=Eikona's Black and Violet Velvet Coats.esp
GameFile68=Elders MCA Add-on.esp
GameFile69=Elders of Vvardenfell.esp
GameFile70=Entertainers_Expanded.esp
GameFile71=Exotic Imports by Westly.esp
GameFile72=Expanded Sounds.esp
GameFile73=ExpandedBirthsigns4Purists.esp
GameFile74=Faction Hellos.esp
GameFile75=Fireflies.esp
GameFile76=Fligg's Slave Mod.esp
GameFile77=Forests of Vvardenfell.esp
GameFile78=GCD Restore Potions Fix.esp
GameFile79=GCD StartScript for Trib or Bloodmoon.esp
GameFile80=GCD settings fairly easy.esp
GameFile81=Galsiahs Character Development.esp
GameFile82=Gatanas Markynaz Dremora Companion - Male.esp
GameFile83=Gondoliers.esp
GameFile84=Gothic Attire Complete v1-1.esp
GameFile85=Gothic&Regal Dresses_1.1.esp
GameFile86=GovernerMansionReplacer.esp
GameFile87=H.E.L.L.U.V.A. Complete Weapons.esp
GameFile88=Hilgya the Seamstress Expansion 1.esp
GameFile89=House of Earthly Delights, Harem Style.esp
GameFile90=IceNioLivRobeReplacerPLUS.esp
GameFile91=Imp_male_weight_fix.esp
GameFile92=Imperial Employment Office.esp
GameFile93=Inn Whisp Wood BM.esp
GameFile94=Investigators_Trib.esp
GameFile95=KRS_VG2.1.esp
GameFile96=KS_Katisha's_Fancy_Threads_1.0.esp
GameFile97=K_Potion_Upgrade_1.2.esp
GameFile98=Korana's Ladies, Companions and Equipment.esp
GameFile99=LCV MCA 4.1 Patch.esp
GameFile100=LGNPC Mods.esp
GameFile101=LadyD_Reduced_Commentary.esp
GameFile102=Lantern replacer By Leeloo.esp
GameFile103=LeFemmArmor.esp
GameFile104=Leaves of Lorien.esp
GameFile105=Lyssia's Adjusted Birthsigns and Classes.esp
GameFile106=Lyssia's Book Collection.esp
GameFile107=Lyssia's Houses, Core Collection.esp
GameFile108=Lyssia's Races, Heads, & Hairs Collection.esp
GameFile109=Lyssia's Ring of Starlight.esp
GameFile110=Lyssia's Treasure Collection.esp
GameFile111=Lyssia's Weapon Collection.esp
GameFile112=MQB-Ice Collection.esp
GameFile113=MW Children Addons.esp
GameFile114=MW2009-Misc Objects.esp
GameFile115=Mashed Lists.esp
GameFile116=Minions of House Dagoth.esp
GameFile117=MixedSignposts.esp
GameFile118=ModMan_windowlights_full_2.esp
GameFile119=MoragTongWritFix.esp
GameFile120=Morrowind Comes Alive Addons.esp
GameFile121=Murderous Dreams_Safe.esp
GameFile122=Myrabell's Clothing Emporium.esp
GameFile123=NPC LCV Schedules 03.esp
GameFile124=Name Change.esp
GameFile125=No-Glo_Revisited.esp
GameFile126=Pearls Enhanced - Colored Pearls Add-on.ESP
GameFile127=Provincial_Bath _Shoppe_v1.esp
GameFile128=Ring Texture Fix.esp
GameFile129=Royal Chargen Calvus add-on.esp
GameFile130=SW_LivingCitiesofVvardenfell03-13Patch.esp
GameFile131=Shadowfox Armor.esp
GameFile132=Sils UCM Collection.esp
GameFile133=Slof's Better Beasts a.esp
GameFile134=Slof's Goth Shop Collection.esp
GameFile135=Soti_KungFu.esp
GameFile136=South Wall.ESP
GameFile137=SpzInteriorDaylight.esp
GameFile138=Starfires NPC Additions ver-1.0.esp
GameFile139=TF_VillaFortuna.esp
GameFile140=TVwofs.esp
GameFile141=Telvanni Robe.esp
GameFile142=The Crimson Wire by Mandamus-EV1.0.esp
GameFile143=The Holiday Mod.esp
GameFile144=The Imperial Legion Badge.esp
GameFile145=The Sable Dragon 1.5.esp
GameFile146=The Shrine of Mephala by Westly.esp
GameFile147=TownSounds.esp
GameFile148=Travel Time 24.esp
GameFile149=UAR_Bloodworm_v1.esp
GameFile150=UAR_ChodalaBoots.esp
GameFile151=Unique Banners and Signs.esp
GameFile152=UniqueFinery_NoRobe.esp
GameFile153=VTA_TravelBM+Trib.esp
GameFile154=Victorian Lace.esp
GameFile155=Waterfall v1.0.esp
GameFile156=Wayside_Inn.esp
GameFile157=Westly Presents-Night Song Armour.esp
GameFile158=Westly Presents_Creed of the Assassin.esp
GameFile159=Westly_Presents_BB_Almalexia_Add_on.esp
GameFile160=Wolf's Eye Birthsign.esp
GameFile161=Zebabi Maren - Gondolier.esp
GameFile162=adamantiumarmor.esp
GameFile163=armor of the dead.esp
GameFile164=dej_plain_paper_fix.esp
A lot of things are merged, but mostly I kept it to merging several similar mods by the same person; the MQB addons, for instance. The merged house mods are:
Abu's Manor
Abu's Retreat
AK_IndarysGreathouse
Archmage's Tower by Antares
Ascadian Ship Home
Ascadian Rose Cottage
Balmora Council Club
Bloodskaal House
bm-house
Clean Princess Factors Estate
Clean TirnaOg
Clean_WH_Well House
Dagonview House
Firemoth Expanded
Japanese House
New Rethan Manor
Patriarch Living Quarters
Princess Pocket Homes
Princess Seyda Neen Shack
Rain's Hand Hall
Seaside Cottage
Solstheim Zelda Estate
Steinthor Hall
temple_apartment
Vivec, St.Delyn Living Quarters [TBBM]
Vodunius_Nuccius_House_V1.1
Xenterra Keep
Most of which I ran together in my last setup without this issue.
Any help would be greatly appreciated!