I got FCOM working but then I installed Qarls Texture Pack 3 Redimized, DarnUi and the following .esms and .eps:

ScreenEffects.esm
EnhancedWeather.esm
Natural_Habitat_by_Max_Tael.esp
EnhancedWeather.esp
Enhanced Water v2.0 HDMI.esp
MIS.esp
MIS New Sounds Optional Part.esp
WindowLightingSystem.esp
P1DkeyChain.esp
FearsomeMagicka.esp
SM Combat Hide.esp
SM Bounty.esp
kuerteeCrimeHasWitnesses.esp
Oblivion XP.esp
ScreenControls.esp
Streamline 2.0.esp

Fcom worked perfectly with my tests, even with better cities but after installing those mods it now crashes when a new or saved game first loads. Even with the mods turned off it still crashes. Any clue on whats wrong?

Did you test after installing each mod? That is way too much to add all at once. That assortment of mods change a great range of things.

1) Did you use OBMM to install DarN? It requires that you apply a few font tweaks to the Oblivion.ini, and the game will not load properly without them
2) ScreenEffects relies on a buggy DLL, OBGE.DLL, but you can replace that by deleting it and installing a fixed version of the v2 DLL http://www.gamesas.com/index.php?/topic/1102453-oblivion-graphics-extender-thread-16/page__view__findpost__p__16126078
3) Upgrade Streamline to the 3.1 open beta (patched) - http://tesivpositive.animolious.com/index.php?page=stabilization_and_optimization_mods#OBSEPlugins
4) Do you have OBSE v18 Stable installed? A number of the mods you have listed there require, as in 90%...

OBSE - http://tesivpositive.animolious.com/index.php?page=obse