When ever I have CTD's like this I do the following:
1) install every mod you are going to use ( this is for a new game / play through )
2) run loot
3) run Wrye Bash and correct load order and make sure all check mars are green, if not drag up or down till they are
4) delete bashed patch and let Wrye Bash make a new one ( for CTD's during a play through )
5) run TES5Edit and verify load order
Deleting the existing bashed patch and making a new one works almost every time, I have tested this extensively in my own play through multiple times. Don't ask me why, but it does work.