I almost found the perfect mod load order for me... Or so it seems anyways, however, I keep crashing over and over again, whenever I go near a major city. It doesn't always happen instantly but within a few minutes of walking around Solitude or Whiterun. It either just CTDs and closes, or alternatively it freezes and I have to use Task Manager to close it. Seems it happens most around the entry of Whiterun and the Solitude bridge, usually after about 7-20 minutes of playing, each time I manually walk to each of the two cities from the starter zone with a fresh new character.

The mod load order is almost perfect for my own playstyle, enough mods to overhaul Skyrim to my tastes but not so needlessly complex like 200+ mods... Only issue is, I suspect I need to figure out which mods I'll have to give up for a stable Skyrim I can actually play.

Can someone please point out which mods you suspect are either causing this issue, or causing compatibility issues with other mods? I even turned off the graphic enhancement mods like the texture packs yet it still happens.

Here are the mods and here's the mod load order.

Falksaar.esm.
Shadow of Morrowind.Esm
SkyrimBordersDisabled.Esm
Campire.Esm
Moonpatch.esm
HighResTexturePack1
HighResTexturePack2
HighResTexturePack3
Degradation.esp
DarkDungeons.esp
Overhaul.esp (UNofficial Morrowloot Skyrim overhaul).\
Overhaul4E.esp
AwakenedMagicka.esp
Rebirth Monster.esp
RealisticWaterTwo.Esp
Morrowloot.esp
Skyrim Immersive creatures.esp
beyond_skyrim.esp
Protected NPCs.esp
KillEssential.esp
BetterQuestObjectives.esp
ESFCompanions.esp
w2salem.esp
Skyrim Immersive Creatures DLC2.esp
AshesOfTheRedMountain.esp
MoonAndStar_Mas.esp
Waves.esp
Tes Arena northkeep.esp
ZKG.esp
SkyrimSewers.esp
tes arena nimalten.esp
LSDarena.esp
RealisticWatertwo - Legendary.esp
Run For Your Lives.esp
moonpatch_questdata.esp
Realistic Water Two - Waves.esp
SkyUI.esp
Rebirth Monsters - Sic Patch.esp
Hunterborn.esp
Immersive Patrolls II.esp
OverhaulDG.esp
ScopedBows.esp
inigo.esp
frostfall.esp
WheelsOfLul.esp
glowtastic.esp
RealisticWatertwo - Dragonborn.esp
Ancient Spells 2.esp
TrueMorrowAtronachShrine.esp
alternate visuals for spell effects.esp
talleflameatronachs.esp
rrhairkhajiit.esp
_tck_SpellCrafting.esp
BetterTreeSapPotions.esp
BetterRedWaterSkooma.esp
TruehardcoeMorrowSkooma.esp
RaceMenu.esp
RaceMenuPlugin.esp
Tribunal Maskes by Zairaam.esp
Pauldrons.esp
Chesko_MorrowindPotionNames.esp
Digitigradeskhajiit.esp
masser_and_secunda_from_morr.esp
Project Castle.esp
Immersive Dawnguard.esp
Immersive Mercenaries.esp
The PaarthunaxDilemma.esp
RealisticNights.esp
RealisticNightsDB.esp
RealisticNightsDG.esp
Watercolor_for_end_RWT.esp
ScopedBows_ArrowTweaks.esp
Magic of the Magna-Ge.esp
DwemerTech - Magic of the Dwarves.esp
RealisticWatertwo - Waves - Dawnguard.esp
Immersive Werewolves.esp
RealisticWaterTwo - Dawnguard.esp
Aethernautics.esp
Immersive Travelers.esp
Immersive Brigans.esp
OldschoolStatsClassesAndClimbing.esp
Quick Start _ Skip The Opening Sequence.esp
Height Adjusted Races.esp
BeastFeetAbilities.esp
spitdiverseguardsskyrim.esp
Skyrim Traits.esp
Blackmarketv2.esp
Dwemer Certified.esp
AWAconquest.esp
RedMountainErupts.esp
VampireNightmares.esp
Character Creation Overhaul.esp
CCO - DYnamic Skill Progression.esp
DwemerOutfit.esp
Protected NPCs Dragonborn.esp
Protected NPCs Dawnguard.esp
EK_LimitedItems.esp
Morrowind Soul Gems.esp
Open Cities Skyrim.esp (Yeah the old version cause no
Hearthfire).
OCS+Skyrim Sewers.esp
Bashed Patch.

Is this loadorder of yours sorted with LOOT?

If not then sort it in LOOT first before doing anything else, but also use this http://www.nexusmods.com/skyrim/mods/52363 (it's safe to use and I use it myself) and if it doesn't help then load the entire loadorder into TES5Edit and check for conflicts plus dirty mods.

First, check your PC and make sure it is capable of handling all the mods you have loaded. (Enough memory available, etc.) That might sound way too simple, but there have been several people complaining about the same type of problem which turned out to be hardware problems. Both Whiterun and Solitude have a lot of NPC's and grapics and your mods add a lot more.