I use an alternate start mod that I made for myself which includes a way to start the mainquest after. As far as I know I did everything right but I wonder if it could somehow contribute. Other than that I use a set essential spell to make sure some quest specific NPCs don't die. I think this might be a cause as well.
Now, I actually wont be able to play Oblivion for the next week starting tonight as I will be away from my computer but I will have internet access. Despite this I hope you guys can put your heads together for me and help me while I am away.
My load order for reference.
Spoiler
Oblivion.esm
EnhancedWeather.esm
Cobl Main.esm
TamrielTravellers.esm
BetterMusicSystem.esm
Unofficial Oblivion Patch.esp
Oblivion Citadel Door Fix.esp
DLCShiveringIsles.esp
Unofficial Shivering Isles Patch.esp
SM Plugin Refurbish - SI.esp
DLCFrostcrag.esp
DLCFrostcrag - Unofficial Patch.esp
SM Plugin Refurbish - FrostCrag.esp
DLCThievesDen.esp
DLCThievesDen - Unofficial Patch.esp
DLCThievesDen - Unofficial Patch - SSSB.esp
SM Plugin Refurbish - ThievesDen.esp
DLCVileLair.esp
DLCVileLair - Unofficial Patch.esp
DLCBattlehornCastle.esp
DLCBattlehornCastle - Unofficial Patch.esp
SM Plugin Refurbish - Battlehorn.esp
DLCHorseArmor.esp
DLCHorseArmor - Unofficial Patch.esp
SM Plugin Refurbish - HorseArmor.esp
DLCOrrery.esp
DLCOrrery - Unofficial Patch.esp
SM Plugin Refurbish - Orrery.esp
DLCSpellTomes.esp
DLCMehrunesRazor.esp
DLCMehrunesRazor - Unofficial Patch.esp
SM Plugin Refurbish - MehrunesRazor.esp
Knights.esp
Knights - Unofficial Patch.esp
SM Plugin Refurbish - Knights.esp
Oblivion XP.esp
kuerteeCleanUp.esp
Side's EAX Control.esp
RefScope.esp
Cobl Si.esp
Cobl Glue.esp
Salmo the Baker, Cobl.esp
Happyhannah's Wines.esp
More_Vegetables.esp
Slof's Horses Base.esp
kuerteeHorseCommands.esp
FarmAnimalsofCyrodiil.esp
TamrielTravellers.esp
TamrielTravellersItemsCobl.esp
TamrielTravellersHorseTextures.esp
ShiveringIsleTravellers.esp
Better Sheogorath.esp
Wrye Shivering.esp
Wrye Shivering Death - Edited.esp
MOBS SI Optional Combat Settings.esp
kuerteeAttributeAndSkillBasedDamageModifiers.esp
Creature Damage Fix.esp
PTActorsCare.esp
PTLessKnockback.esp
PTDoorExploitBegone.esp
vampirism_tweaks_backwards-2216.esp
SM Encumbrance and Fatigue.esp
SupremeMagicka.esp
SM_ShiveringIsles.esp
SM_EnchantStaff.esp
Kyoma's Spell Renamer.esp
Lightweight Potions.esp
Enchantment Enhanced.esp
EnchantmentRestore.esp
Wayshrines Improved.esp
sr_casting_time.esp
sr_casting_hand.esp
Syc_AtHomeAlchemy.esp
Leviathan Soulgems.esp
WNewShockBoltEffects20.esp
PortableOblivionPortal - Edited.esp
SetEssentialActors.esp
Active_Inventory_Spell_1.2.esp
lumi_enchantments.esp
DS Flaming Arrows.esp
SkeletonShaders.esp
AgarMoreVariedSpellEffects.esp
HungerFix.esp
RenGuardOverhaul.esp
LFox No Trespassing.esp
Enhanced Economy.esp
Elys Invest More.esp
Map Marker Overhaul.esp
Map Marker Overhaul - SI additions.esp
MiniMap.esp
Display Stats.esp
SPAWN.esp
kuerteeAutoSaveAndTime.esp
EnhancedWeather.esp
Enhanced Weather - Across-The-Borders Mods Patch.esp
OBSE-Storms & Sound SI - Edited.esp
Get Wet.esp
Rainbows.esp
Enhanced Vegetation [125%].esp
Natural_Habitat_by_Max_Tael.esp
Distant Chapel Bells.esp
New_Sheoth_Palace_LOD_fix-10076.esp
Full Harvest.esp
Harvest [Flora].esp
Harvest [Flora] - DLCFrostcrag.esp
WindowLightingSystem.esp
FlamesRandomLightUOP.esp
All Natural - Real Lights.esp
Echo_ChapelChant.esp
LoadingScreens.esp
Natural Selection.esp
RealisticForceMedium.esp
ChaseCameraMod.esp
VanityCameraSmoother.esp
HorseTurnSpeed-Faster.esp
RealDaysAndMonths.esp
No More Annoying Comments.esp
CDM - Shivering Time.esp
MartinslongswordLeveled.esp
Cliff_RankDependantArenaSpectators.esp
CT-Just Another Combatant.esp
sr_super_hotkeys.esp
Toggleable Quantity Prompt.esp
Lock Bash Omega.esp
DropLitTorchOBSE.esp
Better Bruma Statue.esp
Mayu's Animation Overhaul - Edited.esp
actors_in_charge.esp
ActorsInMadness.esp
ActorsInEmotions.esp
Quest Award Leveller.esp
Book Jackets Oblivion.esp
ImprovedSigns.esp
RoadSigns.esp
HeavenStoneNirn.esp
Ushnar's Re-skinned Hound.esp
EVE_ShiveringIslesEasterEggs.esp
MB - Races and Birthsigns.esp
XtHairs-Eyes.esp
XtRace.esp
XtEquips.esp
XtTwilight.esp
XtTwilightStart.esp
Bashed Patch.esp
XtMaster.esp
EnhancedWeather.esm
Cobl Main.esm
TamrielTravellers.esm
BetterMusicSystem.esm
Unofficial Oblivion Patch.esp
Oblivion Citadel Door Fix.esp
DLCShiveringIsles.esp
Unofficial Shivering Isles Patch.esp
SM Plugin Refurbish - SI.esp
DLCFrostcrag.esp
DLCFrostcrag - Unofficial Patch.esp
SM Plugin Refurbish - FrostCrag.esp
DLCThievesDen.esp
DLCThievesDen - Unofficial Patch.esp
DLCThievesDen - Unofficial Patch - SSSB.esp
SM Plugin Refurbish - ThievesDen.esp
DLCVileLair.esp
DLCVileLair - Unofficial Patch.esp
DLCBattlehornCastle.esp
DLCBattlehornCastle - Unofficial Patch.esp
SM Plugin Refurbish - Battlehorn.esp
DLCHorseArmor.esp
DLCHorseArmor - Unofficial Patch.esp
SM Plugin Refurbish - HorseArmor.esp
DLCOrrery.esp
DLCOrrery - Unofficial Patch.esp
SM Plugin Refurbish - Orrery.esp
DLCSpellTomes.esp
DLCMehrunesRazor.esp
DLCMehrunesRazor - Unofficial Patch.esp
SM Plugin Refurbish - MehrunesRazor.esp
Knights.esp
Knights - Unofficial Patch.esp
SM Plugin Refurbish - Knights.esp
Oblivion XP.esp
kuerteeCleanUp.esp
Side's EAX Control.esp
RefScope.esp
Cobl Si.esp
Cobl Glue.esp
Salmo the Baker, Cobl.esp
Happyhannah's Wines.esp
More_Vegetables.esp
Slof's Horses Base.esp
kuerteeHorseCommands.esp
FarmAnimalsofCyrodiil.esp
TamrielTravellers.esp
TamrielTravellersItemsCobl.esp
TamrielTravellersHorseTextures.esp
ShiveringIsleTravellers.esp
Better Sheogorath.esp
Wrye Shivering.esp
Wrye Shivering Death - Edited.esp
MOBS SI Optional Combat Settings.esp
kuerteeAttributeAndSkillBasedDamageModifiers.esp
Creature Damage Fix.esp
PTActorsCare.esp
PTLessKnockback.esp
PTDoorExploitBegone.esp
vampirism_tweaks_backwards-2216.esp
SM Encumbrance and Fatigue.esp
SupremeMagicka.esp
SM_ShiveringIsles.esp
SM_EnchantStaff.esp
Kyoma's Spell Renamer.esp
Lightweight Potions.esp
Enchantment Enhanced.esp
EnchantmentRestore.esp
Wayshrines Improved.esp
sr_casting_time.esp
sr_casting_hand.esp
Syc_AtHomeAlchemy.esp
Leviathan Soulgems.esp
WNewShockBoltEffects20.esp
PortableOblivionPortal - Edited.esp
SetEssentialActors.esp
Active_Inventory_Spell_1.2.esp
lumi_enchantments.esp
DS Flaming Arrows.esp
SkeletonShaders.esp
AgarMoreVariedSpellEffects.esp
HungerFix.esp
RenGuardOverhaul.esp
LFox No Trespassing.esp
Enhanced Economy.esp
Elys Invest More.esp
Map Marker Overhaul.esp
Map Marker Overhaul - SI additions.esp
MiniMap.esp
Display Stats.esp
SPAWN.esp
kuerteeAutoSaveAndTime.esp
EnhancedWeather.esp
Enhanced Weather - Across-The-Borders Mods Patch.esp
OBSE-Storms & Sound SI - Edited.esp
Get Wet.esp
Rainbows.esp
Enhanced Vegetation [125%].esp
Natural_Habitat_by_Max_Tael.esp
Distant Chapel Bells.esp
New_Sheoth_Palace_LOD_fix-10076.esp
Full Harvest.esp
Harvest [Flora].esp
Harvest [Flora] - DLCFrostcrag.esp
WindowLightingSystem.esp
FlamesRandomLightUOP.esp
All Natural - Real Lights.esp
Echo_ChapelChant.esp
LoadingScreens.esp
Natural Selection.esp
RealisticForceMedium.esp
ChaseCameraMod.esp
VanityCameraSmoother.esp
HorseTurnSpeed-Faster.esp
RealDaysAndMonths.esp
No More Annoying Comments.esp
CDM - Shivering Time.esp
MartinslongswordLeveled.esp
Cliff_RankDependantArenaSpectators.esp
CT-Just Another Combatant.esp
sr_super_hotkeys.esp
Toggleable Quantity Prompt.esp
Lock Bash Omega.esp
DropLitTorchOBSE.esp
Better Bruma Statue.esp
Mayu's Animation Overhaul - Edited.esp
actors_in_charge.esp
ActorsInMadness.esp
ActorsInEmotions.esp
Quest Award Leveller.esp
Book Jackets Oblivion.esp
ImprovedSigns.esp
RoadSigns.esp
HeavenStoneNirn.esp
Ushnar's Re-skinned Hound.esp
EVE_ShiveringIslesEasterEggs.esp
MB - Races and Birthsigns.esp
XtHairs-Eyes.esp
XtRace.esp
XtEquips.esp
XtTwilight.esp
XtTwilightStart.esp
Bashed Patch.esp
XtMaster.esp