These CTD aren't just at random times, they are in specific places. So far I've found them to be: Bleak Falls Borrow, the Dwemer Museum, Ysgramor's Tomb, Arkngthamz, and Nchuand-Zel. Also the undercroft or something like that in Castle Volkihar.
I'm sure there are others, but I haven't found them yet. These place's all seem really random and don't seem to have anything in common.
Since TES5Edit was released during my break, I decided to start using that in conjunction with BOSS and Wrye Bash to clean up the mods I use. I've gone through and cleaned all my active mods (there's still like 4 left, but BOSS didn't detect any problems with them), including the Dawnguard.esm and Update.esm.
Even after all the cleaning I'm still having the exact same CTD's. I figured maybe some script was running in my save file causing the CTD's, so I made a backup of all the scripts in /data/scripts, deleted them and started a new character. I used "coc YsgramorsTomb01" to test and it still crashed. To me, this means it has to be something caused by a mod since it was a completely fresh character. I tried deactivating the Dawnguard.esm because I think that is when I started having problems (not positive on this), but the CTD's still happen in the same specific locations/cells.
I've done just about everything I can think of with the exception of turning all my mods on one by one. If anyone has had a similar experience or knows of how to remedy this I would be so grateful.
Here is my list of mods:
Spoiler
* 00 Skyrim.esm [CRC: C665FD56]
* 01 Update.esm [CRC: 490BBECF]
* 02 Dawnguard.esm [CRC: 11611AC0]
* 03 ETaC - RESOURCES.esm [CRC: 6D4F9941]
* 04 Lanterns Of Skyrim - All In One - Main.esm [CRC: CCF617F4]
* 05 Nchuzzrezar.esm [CRC: 98F7FA69]
* 06 StaticMeshImprovementMod.esp [CRC: 7985AB43]
* 07 Birdsofskyrim.esp [CRC: 53C069A8]
* 08 Carriage1.esp [CRC: 7F4819C4]
* 09 Immersive Battles.esp [CRC: 6CECB1B1]
* 0A Immersive Brigands.esp [CRC: 36958C0C]
* 0B Immersive Patrols.esp [CRC: F79B8FF7]
* 0C Immersive Travelers.esp [CRC: 6A969C81]
* 0D Lanterns Of Skyrim - All In One - Climates of Tamriel - lvl-3.esp [CRC: F610F4BD]
* 0E Lost Art of the Blacksmith.esp [CRC: 8E4BA610]
* 0F SabreFurBag.esp [CRC: 78D9514B]
* 10 CrowdedCities.esp [CRC: 92F9BAD9]
* 11 Archer's.esp [CRC: 8CF9A251]
* 12 Dwemer Goggles & Scouter.esp [CRC: 67C84409]
* 13 Evil MasterMind Armor.esp [CRC: 267E7FAB]
* 14 FaalSizaan.esp [CRC: 050A4F17]
* 15 hothtrooper44_ArmorCompilation.esp [CRC: 53E0D03D]
* 16 Insanity's Sorrow.esp [Version 1.2] [CRC: E8371CEC]
* 17 LostLongSwords.esp [CRC: 8DA6AEE2]
* 18 NarquelionBow.esp [CRC: 4098EBAF]
* 19 nordicrangerarmor.esp [CRC: 31F4AAA9]
* 1A Ritual Armor of Boethiah.esp [CRC: 22EB7172]
* 1B Roman armor and weapons.esp [CRC: 5C3B5B17]
* 1C Roman armor and weapons replacer.esp [CRC: 7F723995]
* 1D Siege Bow & Backpacks.esp [CRC: AFB2F348]
* 1E TCOSS.esp [CRC: 32099B30]
* 1F Tribunal Maskes by Zairaam.esp [CRC: 814BC380]
* 20 Tribunal Robes by Zairaam.esp [CRC: 4BADFB50]
* 21 Vampiric Sword.esp [CRC: 1620B83C]
* 22 Beautiful Riften.esp [CRC: 8D7FB77F]
* 23 Beautiful Whiterun.esp [CRC: 116826C2]
* 24 Breezehome_FullyUpgradable.esp [CRC: 732F2801]
* 25 LakesideHideaway.esp [CRC: EAF818C4]
* 26 Landscaped_Proudspire.esp [CRC: D2E56B09]
* 27 Markarth_plus.esp [CRC: 9EA614CA]
* 28 Nchuzzrezar.esp [CRC: 2A74A714]
* 29 Proudspire Manor Refurbished.esp [Version 1.6] [CRC: D38E8E32]
* 2A RealisticWhiterun.esp [CRC: F869B4D0]
* 2B RiversideLodge.esp [Version 1.3.2] [CRC: 1C4072D1]
* 2C VlindrelArmory v2_Nav.esp [CRC: 5D123005]
* 2D Vjarkell Castle.esp [CRC: BE62E096]
* 2E whiterunMarket.esp [CRC: A41816B0]
* 2F Wickwood.esp [CRC: DEA9CB1B]
* 30 FA Guard Helmet.esp [CRC: 55D907BC]
* 31 Guard Dialogue Overhaul.esp [CRC: 0901147B]
* 32 Realistic werewolf speed.esp [CRC: 6B5D22BB]
* 33 torches for realistic lighting.esp [CRC: 1E87A378]
* 34 ETaC - Villages Complete.esp [CRC: 33943B34]
* 35 ETaC - Morthal.esp [CRC: 91D3DC9A]
* 36 TAVEWindhelm.esp [CRC: BC134DB4]
* 37 3DNPC.esp [CRC: 4299AC8B]
* 38 UFO - Ultimate Follower Overhaul.esp [CRC: A860F39A]
* 39 UFO - Dawnguard AddOn.esp [CRC: 4F7068C8]
* 3A Random Alternate Start.esp [CRC: EEC411A3]
* 3B RAS - Riverwood CharGen.esp [CRC: A16EA630]
* 3C rcrnShaders.esp [CRC: D93FD670]
* 3D RCRNvolumetric.esp [CRC: 54176F89]
* 3E WATER.esp [CRC: FB751550]
* 3F Serana No Hood.esp [CRC: 5F9427A8]
* 40 solitude enhanced.esp [CRC: 53CDB129]
* 41 DarkCoatOfPlates - Credo v4.0.esp [CRC: 355A69F2]
* 00 Skyrim.esm [CRC: C665FD56]
* 01 Update.esm [CRC: 490BBECF]
* 02 Dawnguard.esm [CRC: 11611AC0]
* 03 ETaC - RESOURCES.esm [CRC: 6D4F9941]
* 04 Lanterns Of Skyrim - All In One - Main.esm [CRC: CCF617F4]
* 05 Nchuzzrezar.esm [CRC: 98F7FA69]
* 06 StaticMeshImprovementMod.esp [CRC: 7985AB43]
* 07 Birdsofskyrim.esp [CRC: 53C069A8]
* 08 Carriage1.esp [CRC: 7F4819C4]
* 09 Immersive Battles.esp [CRC: 6CECB1B1]
* 0A Immersive Brigands.esp [CRC: 36958C0C]
* 0B Immersive Patrols.esp [CRC: F79B8FF7]
* 0C Immersive Travelers.esp [CRC: 6A969C81]
* 0D Lanterns Of Skyrim - All In One - Climates of Tamriel - lvl-3.esp [CRC: F610F4BD]
* 0E Lost Art of the Blacksmith.esp [CRC: 8E4BA610]
* 0F SabreFurBag.esp [CRC: 78D9514B]
* 10 CrowdedCities.esp [CRC: 92F9BAD9]
* 11 Archer's.esp [CRC: 8CF9A251]
* 12 Dwemer Goggles & Scouter.esp [CRC: 67C84409]
* 13 Evil MasterMind Armor.esp [CRC: 267E7FAB]
* 14 FaalSizaan.esp [CRC: 050A4F17]
* 15 hothtrooper44_ArmorCompilation.esp [CRC: 53E0D03D]
* 16 Insanity's Sorrow.esp [Version 1.2] [CRC: E8371CEC]
* 17 LostLongSwords.esp [CRC: 8DA6AEE2]
* 18 NarquelionBow.esp [CRC: 4098EBAF]
* 19 nordicrangerarmor.esp [CRC: 31F4AAA9]
* 1A Ritual Armor of Boethiah.esp [CRC: 22EB7172]
* 1B Roman armor and weapons.esp [CRC: 5C3B5B17]
* 1C Roman armor and weapons replacer.esp [CRC: 7F723995]
* 1D Siege Bow & Backpacks.esp [CRC: AFB2F348]
* 1E TCOSS.esp [CRC: 32099B30]
* 1F Tribunal Maskes by Zairaam.esp [CRC: 814BC380]
* 20 Tribunal Robes by Zairaam.esp [CRC: 4BADFB50]
* 21 Vampiric Sword.esp [CRC: 1620B83C]
* 22 Beautiful Riften.esp [CRC: 8D7FB77F]
* 23 Beautiful Whiterun.esp [CRC: 116826C2]
* 24 Breezehome_FullyUpgradable.esp [CRC: 732F2801]
* 25 LakesideHideaway.esp [CRC: EAF818C4]
* 26 Landscaped_Proudspire.esp [CRC: D2E56B09]
* 27 Markarth_plus.esp [CRC: 9EA614CA]
* 28 Nchuzzrezar.esp [CRC: 2A74A714]
* 29 Proudspire Manor Refurbished.esp [Version 1.6] [CRC: D38E8E32]
* 2A RealisticWhiterun.esp [CRC: F869B4D0]
* 2B RiversideLodge.esp [Version 1.3.2] [CRC: 1C4072D1]
* 2C VlindrelArmory v2_Nav.esp [CRC: 5D123005]
* 2D Vjarkell Castle.esp [CRC: BE62E096]
* 2E whiterunMarket.esp [CRC: A41816B0]
* 2F Wickwood.esp [CRC: DEA9CB1B]
* 30 FA Guard Helmet.esp [CRC: 55D907BC]
* 31 Guard Dialogue Overhaul.esp [CRC: 0901147B]
* 32 Realistic werewolf speed.esp [CRC: 6B5D22BB]
* 33 torches for realistic lighting.esp [CRC: 1E87A378]
* 34 ETaC - Villages Complete.esp [CRC: 33943B34]
* 35 ETaC - Morthal.esp [CRC: 91D3DC9A]
* 36 TAVEWindhelm.esp [CRC: BC134DB4]
* 37 3DNPC.esp [CRC: 4299AC8B]
* 38 UFO - Ultimate Follower Overhaul.esp [CRC: A860F39A]
* 39 UFO - Dawnguard AddOn.esp [CRC: 4F7068C8]
* 3A Random Alternate Start.esp [CRC: EEC411A3]
* 3B RAS - Riverwood CharGen.esp [CRC: A16EA630]
* 3C rcrnShaders.esp [CRC: D93FD670]
* 3D RCRNvolumetric.esp [CRC: 54176F89]
* 3E WATER.esp [CRC: FB751550]
* 3F Serana No Hood.esp [CRC: 5F9427A8]
* 40 solitude enhanced.esp [CRC: 53CDB129]
* 41 DarkCoatOfPlates - Credo v4.0.esp [CRC: 355A69F2]
Not many and nothing really major. It may also go without saying, but I'm using the latest patch (though this problem happened with the last patch as well).