I found the more verbatim CS Wiki page that cleared it up. I want to start top>down as http://cs.elderscrolls.com/constwiki/index.php/TES4Edit_Cleaning_Guide says, starting with Jog_X_Mod.esm, for Thievery in the Imperial City; thievery.esp).
I want to make sure I am starting this correctly so this is what I have so far:
1. Only bottom master checkbox is checked, and only oblivion.esm and jog_x_mod.esm are enabled. Since Thievery.esp is part of the mod, do I load that as well first or do jog first, then load thievery.esp and clean that next?
Spoiler
Active Mod Files:00 Oblivion.esm01 Jog_X_Mod.esm02 All Natural Base.esm [Version 1.0]03 Francesco's Leveled Creatures-Items Mod.esm [Version 4.5bSI]04 Francesco's Optional New Items Add-On.esm [Version 4.5bSI]05 Francesco's Optional New Creatures Add-On.esm [Version 4.5bSI]06 Cobl Main.esm [Version 1.72]07 Qarls_Harvest.esm08 CyrodiilUpgradeResourcePack.esm09 BetterMusicSystem.esm0A CURP_Controller.esm0B Progress.esm [Version 2.2]0C HorseCombatMaster.esm0D Unofficial Oblivion Patch.esp [Version 3.3.1]0E Oblivion Citadel Door Fix.esp0F DLCShiveringIsles.esp10 Unofficial Shivering Isles Patch.esp [Version 1.4.0]++ RedBag - Fog.esp11 All Natural.esp [Version 1.0]12 All Natural - SI.esp [Version 1.0]13 Immersive Interiors.esp [Version 0.7]14 Immersive Interiors - Lights Addon.esp [Version 0.7]++ Symphony of Violence.esp15 AmbientTownSounds.esp16 Distant Chapel Bells.esp17 Diverse Voices.esp [Version 0.1a]18 All Natural - Real Lights.esp [Version 1.0]19 Cities Alive At Night.esp1A CampfireBehavior.esp [Version 3.0]1B WindowLightingSystem.esp1C 300_Lore_Dialogue_Updated.esp1D BookTrackerOBSE.esp1E ClocksOfCyrodiil.esp1F Chapel Tithe.esp++ Cyrodilic Brandy.esp20 DarNifiedUI Config Addon.esp21 Display Stats.esp [Version 1.2.2]22 Fishing in Cyrodiil.esp23 Inebriation.esp++ Item interchange - Extraction.esp [Version 0.78]24 kuerteeSittableRocks.esp25 P1DseeYouSleep.esp26 Portable Campsite.esp++ P1DseeYouSleep - Portable Campsite.esp27 Purge Cell Buffers - Loading.esp [Version 1.0.0]28 Q - More and Moldy Ingredients v1.1.esp29 Qarls_Harvest.esp2A Qarls_Harvest addon.esp2B Quest Log Manager.esp [Version 1.3]2C SoT_Holiday.esp2D Willful Resistance.esp [Version 4.0]2E Wyverex - Deployable Traps.esp2F Enhanced Economy.esp [Version 4.3.1]30 Crowded Roads Revisited.esp [Version 1.1]31 Crowded Roads Revisited_ChorrolCheydinhal_5.esp32 Crowded Roads Revisited_GoldRoad_10.esp33 Crowded Roads Revisited_GreenRoad_10.esp34 Crowded Roads Revisited_YellowRoad_10.esp35 PTRoamingNPCs.esp36 FF_Real_Thirst.esp37 Choices and Consequences.esp [Version 2.1]38 Duke Patricks - Friendship Ring For Companion Detection.esp [Version 1.8]39 Map Marker Overhaul.esp [Version 3.6]3A Map Marker Overhaul - SI additions.esp [Version 3.5]3B Improved Hotkeys_Extended.esp [Version 1.1]3C DLCHorseArmor.esp3D DLCHorseArmor - Unofficial Patch.esp [Version 1.0.5]3E DLCOrrery.esp3F DLCOrrery - Unofficial Patch.esp [Version 1.0.3]40 DLCVileLair.esp41 DLCVileLair - Unofficial Patch.esp [Version 1.0.5]42 P1DseeYouSleep - DLCVileLair.esp43 DLCMehrunesRazor.esp44 DLCMehrunesRazor - Unofficial Patch.esp [Version 1.0.4]45 DLCSpellTomes.esp++ DLCSpellTomes - Unofficial Patch.esp [Version 1.0.1]++ MaleBodyReplacerV4.esp46 ACCCGR SI.esp++ CM_Better Wine.esp++ FineWeapons.esp++ RustyItems.esp47 WarriorBandages_V2.0.esp48 Thieves Arsenal.esp++ Thieves_Arsenal_Patch_033010.esp49 Slof's Horses Base.esp4A kuerteeHorseCommands.esp4B DLCThievesDen.esp4C DLCThievesDen - Unofficial Patch.esp [Version 1.0.5]4D DLCThievesDen - Unofficial Patch - SSSB.esp [Version 1.0.4]4E Francesco's Optional Files 1.esp4F Francesco's Optional Files 2.esp50 Francesco's Optional Files 4.esp51 Cobl Glue.esp [Version 1.72]52 Cobl Si.esp [Version 1.63]53 FF_Real_Thirst, Cobl.esp++ Cobl Tweaks.esp [Version 1.44]54 Bob's Armory Oblivion.esp55 OBSE-Storms & Sound SI.esp56 Creatures Alive v1.3.esp57 kuerteeWanderingEncounters.esp58 TIE.esp [Version 1.37]59 TIE+Frans NPC Inventory.esp [Version 1.0]5A Lock Bash Omega.esp [Version 1.5]5B Enhanced Quest Roleplaying.esp [Version 2.03]5C cyrodiil transportation network 1.3 wz.esp5D BHC_Expanded.esp [Version 1.2]5E Duke Patricks - Bottle Shoot Archery Practice.esp5F Extended Imperial City Version 1.0.esp60 FuseSnailRacing.esp61 Kragenir's Death Quest.esp62 KDQ - Rural Line Additions.esp63 Corpse_Kvatch.esp64 LetThePeopleDrink.esp [Version 2.5]65 KragenirsDeathQuest-LetThePeopleDrink patch.esp66 Region Revive - Lake Rumare.esp67 TheElderCouncil.esp68 TheElderCouncil_TempleOfTheOne.esp69 TEC_4ERA_Dialog_Filter.esp6A thievery.esp6B thievery - EE patch.esp [Version 4.2]6C Travelers Inns.esp6D VaultsofCyrodiil.esp6E Window Entrances 1.0.esp6F za_bankmod.esp70 DLCBattlehornCastle.esp71 DLCBattlehornCastle - Unofficial Patch.esp [Version 1.0.4]72 BattlehornCastleEnhanced.esp73 Lynges_Thieves_Highway-10256.esp74 DLCFrostcrag.esp75 DLCFrostcrag - Unofficial Patch.esp [Version 1.0.4]76 Knights.esp77 Knights - Unofficial Patch.esp [Version 1.0.9]78 SM Plugin Refurbish(Merged).esp [Version 1.30]79 Choices and Consequences - SM Plugin Refurbish - Orrery.esp [Version 2.0]7A AFK_Weye.esp [Version 2.1.COBL]7B Rumare-AFK_Weye Patch.esp [Version 2.0]7C ElsweyrAnequina.esp7D road+bridges.esp [Version 4.5.7]7E Feldscar.esp [Version 1.0.4]7F Vergayun.esp [Version 1.0.5]80 Faregyl.esp [Version 1.0.10]81 Faregyl+Anequina Patch.esp82 Molapi.esp [Version 1.0]83 xuldarkforest.esp [Version 1.0.5]84 xulStendarrValley.esp [Version 1.2.2]85 xulTheHeath.esp86 XulEntiusGorge.esp87 xulFallenleafEverglade.esp [Version 1.3.1]88 xulColovianHighlands_EV.esp [Version 1.2.1]89 xulChorrolHinterland.esp [Version 1.2.2]8A xulBeachesOfCyrodiilLostCoast.esp [Version 1.6.4]8B KragenirsDeathQuest-LostCoast patch.esp8C xulBravilBarrowfields.esp [Version 1.3.2]8D xulLushWoodlands.esp [Version 1.3]8E xulAncientYews.esp [Version 1.4.3]8F xulAncientRedwoods.esp [Version 1.6]90 xulCloudtopMountains.esp [Version 1.0.3]91 KragenirsDeathQuest-CloudtopMountains patch.esp92 xulArriusCreek.esp [Version 1.1.3]93 xulPatch_AY_AC.esp [Version 1.1]94 xulRollingHills_EV.esp [Version 1.3.2]95 KragenirsDeathQuest-RollingHills patch.esp96 xulPantherRiver.esp97 xulRiverEthe.esp [Version 1.0.2]98 xulBrenaRiverRavine.esp [Version 1.1]99 xulImperialIsle.esp [Version 1.6.5]9A Fuses Snail Racing Unique Landscapes Imperial Isle patch.esp9B RegionReviveLakeRumare-ImperialIsle patch.esp [Version 1.3.3]9C xulBlackwoodForest.esp [Version 1.1.0]9D xulCheydinhalFalls.esp [Version 1.0.1]9E xulAspenWood.esp [Version 1.0.2]9F xulSkingradOutskirts.esp [Version 1.0.1]A0 xulSnowdale.esp [Version 1.0]A1 NRB4+UL-II+LtPD Patch.esp [Version 3.0.1]A2 bartholm.espA3 bartholm - EE patch.esp [Version 4.2]A4 RR - LTPDPatch.espA5 NRB4+RR Patch.esp [Version 2.1]A6 Harvest [Flora].esp [Version 3.0.0]++ Harvest [Flora] - Shivering Isles.esp [Version 3.0.0]++ Harvest [Flora] - DLCVileLair.esp [Version 3.0.0]A7 Harvest [Flora] - DLCFrostcrag.esp [Version 3.0.0]A8 HUD Status Bars.esp [Version 0.9]A9 DecoratorAssistant with OBSE v1.1.espAA DropLitTorchOBSE.esp [Version 2.4]AB DS Storage Sacks.esp [Version 1.21]AC Dungeon Actors Have Torches 1.6 CT.espAD Exterior Actors Have Torches 1.3 CT.espAE GP_Lockpicks.esp [Version 1.5]++ Hurt Me Bad Traps.espAF ImprovedSoulgems.esp [Version 1.11]B0 kuerteeInventoryIsABackpack.espB1 P1DkeyChain.esp [Version 5.00]B2 PersuasionOverhaul.esp [Version 1.43]B3 ReneerNPCNameMod.espB4 RenCorpseMod.espB5 kuerteeGoldIsAnInventoryItem.espB6 Salmo the Baker, Cobl.esp [Version 3.08]B7 SetsunaDummyTraining.espB8 talkwithyourhands2.espB9 Toggleable Quantity Prompt.esp [Version 3.1.1]BA kuerteeAlternativesToDeathAndReload.espBB Enhanced Economy - House prices.esp [Version 1.0]BC Roleplaying Dialogues.espBD Quest Award Leveling.espBE Quest Award Leveling SI.espBF Alternate Start Revamped.espC0 RealisticFatigue.espC1 RealisticHealth.espC2 Real Injury.espC3 RealisticForceMedium.espC4 ReneerKeyLockMod.espC5 RealSleepExtended.esp [Version 2.5]C6 Duke Patricks - Nosferatu Class Vampires.esp [Version y]C7 RefScope.esp [Version 2.0.2]C8 Syc_AtHomeAlchemy.espC9 RshAlchemy.espCA RshAlchemyRecipes.espCB Lightweight Potions.esp [Version 1.1]CC Realistic Sneak for NPCs.esp [Version 1.04]CD StealthOverhaul.espCE ZumbsLockpickingMod - OBSE.espCF ZumbsLockpickingMod - Hide Difficulty Addon.espD0 RenGuardOverhaul.espD1 sycSHOUT.esp [Version 1.02]D2 kuerteeClothingMatters.espD3 Enhanced Grabbing.esp [Version 0.5]D4 Duke Patricks - Double Arrow Nock Shot.esp [Version 1.5.1a]D5 Deadly Reflex 5 - Timed Block with no damage or durability changes.espD6 DeadlyReflex 5 - Combat Moves.espD7 kuerteeNPCsYield.espD8 Duke Patricks - Near Miss Magic And Arrows Alert The Target.esp [Version 7.1]D9 Duke Patricks - Actors Can Miss Now.espDA Duke Patricks - Fresh Kills Now Alert The NPCs.esp [Version 4]DB MM_AlchemyPotions.espDC BFG's Enhanced Armory.espDD Intelligence Overhaul.espDE nGCD.esp++ nGCD Skeleton Key.espDF ProgressGSD.esp [Version 2.0]E0 ProgressMBSP.esp [Version 2.0]E1 ProgressSBSP.esp [Version 1.0]E2 ProgressRBSP.esp [Version 1.0]E3 ProgressRacial.espE4 ProgressArmorer.esp [Version 1.0]E5 immersive_caves_auto.esp** Let There Be Darkness - Cyrodiil + SI.esp** Let There Be Darkness - Knights.esp** Let There Be Darkness - Mehrunes Razor.esp** Let There Be Darkness - Thieves Den.esp** Let There Be Darkness - The Elder Council.esp** Let There Be Darkness - Thievery.esp** Let There Be Darkness - Elsweyr.esp** Let There Be Darkness - UL Colovian Highlands.esp** Let There Be Darkness - UL Lost Coast.esp** Let There Be Darkness - UL Brena.esp** Let There Be Darkness - UL Blackwood Forest.esp++ Item interchange - Placement.esp [Version 0.78]++ Item interchange - Placement for Frostcrag.esp [Version 0.78]++ Item interchange - Option, Ingredients in Bulk.esp [Version 0.78]E6 Stat Restore.esp++ Cobl Races - Balanced.esp [Version 1.52]E7 MM_TrainingCost2.espE8 Really Immersive Messages.espE9 Visual Enchantments LessFire.esp** Enhanced Economy - Soulgems.esp [Version 4.2.2]EA Real Hunger, Cobl.esp [Version 1.6.1]EB MagicDefence.esp++ All Natural - SI Settlements NIW Support.espEC ExperienceBasedTraining.esp++ All Natural - Bravil Mages Fix.espED Region_Revive_-_Lake_Rumare_FuseSnailRacing_Patch.espEE Cyrodiil Training Center.esp** NRB4 Standard Road Record.esp++ Cobl Filter Late MERGE ONLY.esp [Version 1.53]EF Cobl Silent Equip Misc.esp [Version 01]** All Natural - Indoor Weather Filter For Mods.esp [Version 1.0]F0 LandMagicPatch.espF1 Duke Patricks - Combat Archery.esp [Version 3.2]++ Duke Patricks - BASIC Script Effect Silencer.espF2 Bashed Patch, 0.espF3 Colored Map for Elsweyr 1.1.espF4 kuerteeCleanUp.espF5 Oblivion Graphics Extender Support.esp [Version 0.2]