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To properly place SoT you should sort your mod list to look similar to this one.
The Skyrim Unofficial Patches order is taken straight from their Nexus page.
Note: If you use OBIS (Organized Bandits of Skyrim) you MUST place all OBIS files under SoT.
The following is (basically) the proper load order:
Skyrim.esm
Update.esm
USKP
Dawnguard.esm
UDGP
Hearthfires.esm
UHFP
Dragonborn.esm
UDBP
[Other ESMs]
Official hi-res DLC *Best to not use any high-def packages in script heavy modded games
UHRP
SleepingDangers-SandsofTime
[Other ESPs].....
.....
.....
SoTAntiCDT
SoT addons
SoT patches
Bashed patch (if used)
OBIS (Optional, but highly recommended)
OBISDB (if used)
Specialty followers (such as Vilja by Emma or Inigo by Smartbluecat)
AI Limit Increaser (always load at ABSOLUTE bottom if used--not needed if SoT is installed.)