1-st, i would suggest you to check your system drivers, and try to update them to a lates once. 2-nd i was facing the same problem you are, and the problem was, that i have increased memory in bios from auto to 3200 or 3000. This was causing the CTD in skyrim for me. Moving back to auto resolved this problem. Not sure if this will work for you, since i dont even know you pc setup and how you working on it. But if you are saying that previously everything was fine, then 95% it something with your system itself and not mods. Also try to start new game, if you still will receive CTD to desktop from the start, then it's probably not a mods problem.