I seem to have found a solution to this problem. see fourth comment for details.
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So yeah, not matter what I've tried "Way of the Voice" will not start after killing the first dragon and becoming thane of whiterun. I am currently on my third new game after disabling some mods I thought might be causing this but it's happened again.
The only mod in this list I can think of that might be doing this is "The Choice is Yours" but from the mod page it doesn't seem to edit anything related to the MQ.
Load order exported from NMM:
Skyrim.esm=1
Update.esm=1
Unofficial Skyrim Patch.esp=1
Dawnguard.esm=1
Unofficial Dawnguard Patch.esp=1
HearthFires.esm=1
Unofficial Hearthfire Patch.esp=1
Dragonborn.esm=1
Unofficial Dragonborn Patch.esp=1
Skyrim Project Optimization - No Homes - Full Version.esm=1
ClimatesOfTamriel.esm=1
JSwords.esm=0
HighResTexturePack01.esp=1
HighResTexturePack02.esp=1
HighResTexturePack03.esp=1
Bethesda_Hi-Res_Optimized.esp=1
Unofficial High Resolution Patch.esp=1
ClimatesOfTamriel-Dragonborn-Patch.esp=1
AHZmoreHUD.esp=1
ArvakLesserPower.esp=1
WetandCold.esp=1
FISS.esp=1
ClimatesOfTamriel-Dawnguard-Patch.esp=1
Better Summoning Visuals - TheGreyLight.esp=1
dD-No Spinning Death Animation.esp=1
Brawl Bugs CE.esp=1
Beards.esp=1
SkyTEST-RealisticAnimals&Predators-Dawnguard.esp=1
Bounty Gold.esp=1
ClimatesOfTamriel-Nights-Level-3.esp=1
DeadlyCombat.esp=1
Better Dynamic Snow.esp=1
DynamicPotions.esp=1
dD - Enhanced Blood Main.esp=1
dD-Dragonborn-Dawnguard-EBT Patch.esp=1
FFS-Scimitar.esp=1
NB-Scars.esp=1
Guard Dialogue Overhaul.esp=1
aMidianborn_Skyforge_Weapons.esp=1
RaceMenuPlugin.esp=1
HarvestingAnimation.esp=1
Footprints.esp=1
iHUD.esp=1
SplashofRain.esp=1
fNPCHealthLevelBonus_-1.esp=0
fNPCHealthLevelBonus_-2.esp=0
fNPCHealthLevelBonus_-3.esp=0
fNPCHealthLevelBonus_-4.esp=0
fNPCHealthLevelBonus_-5.esp=1
fNPCHealthLevelBonus_0.esp=0
JSwords_Load_Screens.esp=0
LFArmors.esp=1
HarvestOverhaul.esp=1
Moss Rocks.esp=1
Headtracking.esp=1
RaceMenu.esp=1
Clear Skies Fix - CoT version.esp=1
ShieldProtectFromMagic.esp=1
Wandererarmor.esp=1
RelightingSkyrim-FULL.esp=1
SMIM-FarmhouseFlickeringFix.esp=1
Skill Config.esp=1
Better Stealth AI for Followers.esp=1
SkyFalls + SkyMills + DG + DB.esp=1
SkyFalls Dragonborn Small waterfalls.esp=1
RealisticWaterTwo.esp=1
Book Covers Skyrim.esp=1
Complete Crafting Overhaul_Remade.esp=1
Insanity's Iron Bow.esp=1
NoAutoSkillBooks(Better).esp=1
SkyTEST-RealisticAnimals&Predators.esp=1
Remove Interior Fog V2 - Full Version.esp=1
RealisticWaterTwo - Legendary.esp=1
SkyUI.esp=1
dD - Realistic Ragdoll Force - Medium.esp=1
SMIM-DragonbornTernFix.esp=1
SMIM-DungeonsCliffsIceSkirts.esp=1
SMIM-FurnitureChestSnowFix.esp=1
AlwaysPickUpBooks.esp=1
Stealth Skills Rebalanced_COMPLETE.esp=1
StormLord.esp=1
TakeNotes.esp=1
TheChoiceIsYours.esp=1
RealisticWaterTwo - Waves.esp=1
Immersive Dragonborn.esp=1
SMIM-ShackRoofFixesDragonborn.esp=1
JSwordsDistributionBalancePlugin.esp=0
SkaalHeavyArmor.esp=1
SkyTEST-RealisticAnimals&Predators-Dragonborn.esp=1
SMIM-ShackRoofFixes.esp=1
CompanionArissa.esp=1
Immersive Battles.esp=1
Immersive Travelers.esp=1
Immersive Patrols.esp=1
Immersive Mercenaries.esp=1
HoldBorderBanners.esp=1
Hunterborn.esp=1
Hunterborn_Dawnguard-Patch.esp=1
Immersive Dawnguard.esp=1
RealisticWaterTwo - Waves - Dawnguard.esp=1
Immersive Werewolves.esp=1
iNeed.esp=1
Immersive Brigands.esp=1
Equipping Overhaul.esp=1
mcCampingLite.esp=1
AlternativeCraftingSystem.esp=1
mjhReducedGoldRewards.esp=1
TheChoiceIsYours_Dawnguard.esp=1
Immersive Factions.esp=1
RGMsAlchemistsCompendium.esp=1
TorchRadius.esp=1
Unique Uniques.esp=1
WetandCold - Ashes.esp=1
_magehood.esp=1
Warburg's 3D Paper World Map - Texture 1.esp=1
Warburg's 3D Paper World Map - Dragonborn.esp=1
warburg's 3d paper world map - dawnguard.esp=1
This load order was set by LOOT.
Anyone got any idea what's going on?