I have been searching the whole internet for solutions to my issue without success. However, now I have re-installed the whole game and is now on vanilla skyrim. At specific places where I would get constant CTD (Sky Haven Temple) with my modded lvl 45 Imperial, I no longer get the crash with a newly created character. I'm not a modder but in my experience the whole thing that created this mess was the patch conflicting with mods. This would make the save corrupt and the CTD:s not fixable. Unless you have an old save before you updated skyrim i'm afraid you will have to start over. Please tell me if i'm way over my head or I somewhat narrowed it down...