The question is... what ones? Being only a novice modder myself, I find myself mystified by what I must do, so I think I'll leave it up to you more advanced modders.
Here is my mod list from mlox. I will clarify the unknowns I have created to help with the suggestions you give me.
_001_ Morrowind.esm_002_ Tribunal.esm_003_ Bloodmoon.esm_004_ Beauty_Pack.esm_005_ Better Heads.esm_006_ Weapon Rotate.esm_007_ Assassins Armory.esm_008_ Book Rotate.esm_009_ GDR_MasterFile.esm_010_ Texture Fix 1.6.esm_011_ Havish.esm_012_ The Wilderness Mod 2.0 T & B.esm_013_ SG-MW-ecology-BM.esm_014_ MCA.esm_015_ The Undead.esm_016_ MW_Children_1_0.esm_017_ Better Heads Tribunal addon.esm_018_ Better Heads Bloodmoon addon.esm_019_ BT_Whitewolf_2_0.esm_020_ ?exa's Dwemer Alchemy V2 (EN).esm_021_ abotWaterLife.esm_022_ The Juggernaut v1.2 (D).esp_023_ LGNPC_NoLore_v0_83.esp_024_ LeFemmArmor.esp_025_ The Goblin Lab v1.1.esp_026_ Of Love and Ignorance.esp_027_ BM-Fixes.esp_028_ Bloated Morrowind.esp_029_ Haldenshore_1.2.esp_030_ Nymeria's Monthly Respawn.esp_031_ Ruins of Serpenthold.esp_032_ Clean Solstheim_Castle_v1.1.esp_033_ DagonFel_Well_v2.esp_034_ Clean SCastle_Halvart_Beauty.esp_035_ Clean SCastle_LoKKen_Patch.esp_036_ ShockCenturionCompanion_TB_V12.esp_037_ Suran Extended Family.esp_038_ BM_CatCompanions1_0.esp_039_ WolfCompwhite_ver3_0.esp_040_ Better MCA 5.0 Lovesounds 1.0.esp_041_ frostmoth_repaired_v0_31.esp_042_ BB_Clothiers_of_Vvardenfell_v1.1.esp_043_ Adamantium Helm of Tohan Replace.esp_044_ Vampiric Citadel & New Armors v1.1.esp_045_ ale_clothing_v1.esp_046_ P.R.E. v4.0.esp_047_ Seraphs - Water.esp_048_ Nudity Greeting Expansion V1.esp_049_ TelMagus.esp_050_ TelMagus-Grazelands.esp_051_ TelMagus-Ingredients-TB-BM.esp_052_ Clean_Necromantic_Robe_V2.esp_053_ Moon-and-Star.esp_054_ sixy Daedric Armor v1.1.esp_055_ Vivec_Voice_addon TRIBUNAL.esp_056_ Martial Code.esp_057_ SSlave_Companions.esp_058_ Better Bodies.esp_059_ SG_chefik.esp_060_ Clean Telvanni_Robe_V2.esp_061_ Ice_CNS_FemaleTelvanniRobeV2.esp_062_ Ice_CNS_FemaleNecromanticRobe.esp_063_ MCA Stealth Clothing.esp_064_ BirthsignsGalore.esp_065_ Textured_Signs.esp_066_ Vivec_Expansion_v1.1.esp_067_ Complete Morrowind - Tribunal & Bloodmoon.esp_068_ VOORHEES_AldIndoril2.esp_069_ Sea_of_Solstheim.esp_070_ sg_prettykitties.esp_071_ Realistic Weather v2.0.esp_072_ Key Replacer Trib & BM.esp_073_ Richer Traders.esp_074_ NoReflectTribunal.esp_075_ Almalexia_Voicev1.esp_076_ Dulsya Isle.esp_077_ Weapon Rotate - Tribunal.esp_078_ Morrowinter.esp_079_ Morrowinter Tribunal.esp_080_ Weapon Rotate - Bloodmoon.esp_081_ Weapon Rotate - Vendors.esp_082_ abotWhereAreAllBirdsGoing.esp_083_ MW_family1_0.esp_084_ All Boats and Striders.esp_085_ Ancient_Moonstone_v14.esp_086_ PlayableDremoraV11.esp_087_ Weather Stones.esp_088_ Naked Nerevarine.esp_089_ Dwemer Book's-TR.esp_090_ SG-MW-ecology-BM-plugin.esp_091_ PC VOICE COMPLETEv1.8.esp_092_ Necro Armor v1_0.esp_093_ R.D.'s Clothing Placement.esp_094_ MWE_Base.esp_095_ Book Jackets - Morrowind - BookRotate.esp_096_ Book Rotate - Tribunal v5.3.esp_097_ Book Rotate - Bloodmoon v5.3.esp_098_ Assassins Armory - Unofficial Patch 7.7.esp_099_ Clean Granny Claus' Christmas Gifts.esp_100_ The Hidden Pathway 2.0.esp_101_ adamantiumarmor.esp_102_ Clean Better Daedric.esp_103_ Assassins Armory - No Scripts.esp_104_ LOCH_Red_Velvet_Dress_1.1.esp_105_ Tales of the Bitter Coast.esp_106_ Archmagister_robe.esp_107_ Clean max & minimum 2.esp_108_ Magic Grenades(Doublechance).esp_109_ BalmoraWaterfal01_0808.esp_110_ RKWerewolf.esp_111_ IceBradyHurdyRobeReplacerPLUS.esp_112_ Silt_Striders_Are_In_Vvardenfell.esp_113_ Lilarcor_v4-1.esp_114_ Thirsk Expanded Family.esp_115_ The Holiday Mod.esp_116_ The Masks of the Gods.esp_117_ Stan Better Bodies Clothing.esp_118_ BAR_Solstheim Seaside Cabin.esp_119_ ale_clothing_v0.esp_120_ abotGuars.esp_121_ AreaEffectArrows.esp_122_ NoReflectMorrowind.esp_123_ NoReflectBloodmoon.esp_124_ IoC_Clean_FullV1.0.esp_125_ ARJAN_A_Lords_Men_v2.0.esp_126_ New Hair Styles for Human Races.esp_127_ Armor Mannequin.esp_128_ Assassins Armory - Arrows.esp_129_ Clean THFFTribBM_FINAL.esp_130_ DragonRecognition.esp_131_ DN-GDRv1.esp_132_ Clean sixy_Black_Collar_Dress_v.1a.esp_133_ Dragonwarrior light armor.esp_134_ LGNPC_Secret_Masters.esp_135_ Clean Vivec's Sanctum.esp_136_ Dark Elf Hair Styles.esp_137_ TF_skull_landmarks_v1.esp_138_ Dagoth Gares_Voice_addon v1.1.esp_139_ LGNPC_Vivec_Redoran_v1_3.esp_140_ ab01Wilderness2.1patch.esp_141_ Cleaned_Pearl_Palace_v1.esp_142_ CM_Partners_3.0.esp_143_ LGNPC_SM_MCA5.esp_144_ Daedric Pants.esp_145_ EBQ_Artifact.esp_146_ Ice_Wolf_Cuirass_Mod.esp_147_ Ice's BM Ice & NordicMail.esp_148_ HUB v1.0.esp_149_ Ald-Vendras_V31-LoKKen-SC.esp_150_ A Call to Issilar.esp_151_ Nolore_Fixes.esp_152_ Booty.esp_153_ Lgnpc_SN.esp_154_ LGNPC_GnaarMok_v1_10.esp_155_ LGNPC_AldVelothi_v1_20.esp_156_ Elf-Human_Hair_Conversion.esp_157_ LGNPC_MaarGan_v1_11.esp_158_ LGNPC_HlaOad_v1_32.esp_159_ Havish - Scimitar Update.esp_160_ Shadow Shield Replacer.esp_161_ Yagrum Advanced 2.0.esp_162_ Heaven's Lookout.esp_163_ The Neverhalls.esp_164_ Less_Generic_Bloodmoon.esp_165_ Better Bloat.esp_166_ New Argonian Bodies - Clean.esp_167_ New Khajiit Bodies - Clean.esp_168_ Aldbarrow.esp_169_ Trouble at Sea.esp_170_ Havish Mini Patch.esp_171_ LGNPC_Aldruhn_v1_13.esp_172_ DN_AshVampires.esp_173_ LGNPC_Pelagiad_v1_13.esp_174_ LGNPC_TelMora_v1_11.esp_175_ Guarded GhostGate.esp_176_ LGNPC_Khuul_v2_01.esp_177_ LGNPC_VivecFQ_v2_03.esp_178_ LGNPC_TelUvirith_v1_10.esp_179_ k_weather (louder sounds).esp_180_ Japanese_House.esp_181_ k_howareyou.esp_182_ Dwemer Sentinel.esp_183_ LGNPC_Secret_Masters_v1_21.esp_184_ Extra_Classes.esp_185_ hidaway001.esp_186_ Kaylas_Kick-Knacks.esp_187_ LGNPC_Indarys_Manor_v1_45.esp_188_ Book Jackets - Tribunal - BookRotate.esp_189_ Book Jackets - Bloodmoon - BookRotate.esp_190_ A Portcullis for Pelagiad (v1.1).esp_191_ A Portcullis for Hawkmoth (v1.1).esp_192_ A Portcullis for Moonmoth (v1.1).esp_193_ AV_female_armor.esp_194_ Less_Generic_Nerevarine.esp_195_ AV_fem_armor_Trib.esp_196_ A Portcullis for Wolverine Hall (v1.0).esp_197_ Mournhold Expanded COM NC.esp_198_ AA_DwemerFlying Fortress.esp_199_ AV_fem_shirts.esp_200_ MWE_Combat.esp_201_ Zebabi Maren - Gondolier.esp_202_ THTWG - Harder Version.esp_203_ Anya's Directions.esp_204_ LGNPC_VivecRedoran_v1_42.esp_205_ LGNPC_PaxRedoran_v1_12.esp_206_ LGNPC_SoulSicknessPatch_v1_00.esp_207_ Assassins Armory - Bolt Rifles.esp_208_ DN_IceBlade.esp_209_ Hlaalu Vault Extended.ESP_210_ BT_Lokken_child1.esp_211_ Give your orders v13.esp_212_ Telvanni Vault Extended.ESP_213_ Ald Redaynia Extended COM.esp_214_ Complete Morrowind TB & BM - Replacer.esp_215_ Creatures X_Edit.esp_216_ Psy_UniqueDremora_T.esp_217_ Antares' Big Mod 5.esp_218_ Painkiller's Lucky Coin.esp_219_ Morrowind Abodes.ESP_220_ Morrowind Fixes.ESP_221_ SR-Speechcraft What Not to Say.ESP_222_ Azriel Addon.esp_223_ South Wall.ESP_224_ Clean Welcome to the Arena!.ESP_225_ UF_HortRobeF001.esp_226_ DA_Sobitur_Facility_Clean.ESP_227_ Sentinel-V-1.3.esp_228_ DA_Sobitur_Quest_Part_1 Clean.esp_229_ DA_Sobitur_Quest_Part_2 Clean.esp_230_ MCA - Guards Patch.ESP_231_ DA_Sobitur_Repurposed_1.ESP_232_ MCA - COV Addon.esp_233_ DA_ArkFrzanch_Ruins.ESP_234_ AAG_StatusBars.esp_235_ Unique Jewelry and Accessories.esp_236_ fw_malcha_v50.esp_237_ R.D.'s Stuff.esp_238_ SW_MCA5.2_Patch.esp_239_ Less_Generic_Tribunal.esp_240_ UniqueFinery.esp_241_ daedric tower.esp_242_ Lore Correct Armor.ESP_243_ SH Heroines' Outfits.ESP_244_ BUUG Alchemy- Bloodmoon.esp_245_ BUUG Alchemy- Tribunal.esp_246_ Weapon Tweaks 2nd.ESP_247_ master_index.esp_248_ Blackstone Manor.esp_249_ Travel Addon-DagonFelMill-V1.esp_250_ A Hermit's Request.esp_251_ Better Propylons.ESP_252_ Better Propylons MI.ESP_253_ female ranger armor_m001.esp_254_ Animated Morrowind 1.0.esp_255_ Uvirith's Legacy_BETA1.10.esp_256_ Fast Eddie Fix v .0001.esp_257_ The Blind Heretic.ESP_258_ The Imperial Legion Badge.esp_259_ The Sable Dragon 1.5.esp_260_ DA_Sobitur_YA_Compatibility.ESP_261_ Armor Additions.ESP_262_ Uvirith's Legacy Book Jackets Add-on.esp_263_ MDP Compilation.ESP_264_ DagonFel Mill 1.4-F.esp..esp_265_ Building Up Uvirith's Legacy1.1.ESP_267_ Twin Blades of Azzinoth.esp_266_ Mashed Lists.esp
Now, for the unknowns:
R.D.'s Stuff - These are my own personal creations. I often have to edit this so I try to keep it out of everything else, though its currently dependent on the three original master files and Book Rotate, and a couple other mods such as the Secret Getaway (hidaway001.esp).
R.D.'s Clothing Placement - Back before I learned that the Construction Set can only auto-load so many masters, I wanted certain clothes from Morrowind Comes Alive for my PCs available, but I couldn't without killing someone/cheating. But I didn't know about the rules concerning master file loading, so I couldn't get it to open more than once. Its dependent on Morrowind Comes Alive.
Armor Additions - An already-merged plugin for mods that add armor sets and such to the game. I try to add new armor plugins to it whenever possible.
Weapon Tweaks - The same as Armor Additions, but for weapon modifications. I try to add new weapon plugins to it whenever possible.
Morrowind Abodes - These are all of the "Your (townnamehere) Residence" mods created by Morrowind Abodes, merged into a single plugin.
Morrowind Fixes - Mods that involve fixing overlooked glitches in the game, such as improper body part setting or dialogue errors and things of that nature.
Please note that my copy of Guarded Ghostgate is currently modified to be compatible with Complete Morrowind, as activating them both normally removes half a bridge and plants a tree through a platform. I dunno if that'll affect anything important. Also, it'd probably be best if I did NOT merge any mods that update frequently, such as abot's Guars, Water Life, and Bird mods.
So, I'm open to suggestions:
What should I do?