To throw in my 2 cents on CTDs...
I've recently installed SE (correctly, with latest pluggy and everything) and almost immediately I started getting black screens. Not nVidia black screen where you don't see absolutely nothing, but dark-gray screen with hands and weapon visible from first person perspective. I'm not too certain, but I think it is actually fake first person perspective. I've installed unnecessary violence recently, so I'm pretty much confused about what is going on with my bunch of mods..
Anyway, among tedious CTDs, one error message actually managed to get through. It had to do with xvid(something).dll, so I'm thinking that there is a illusive codec issue. And if it is a codec, then it doesn't necessarily have to mean that it is video-related issue. Actually, in oblivion mid-game, there isn't much need for video decoding... but... audio is being decoded all the time, and I did notice that there are number of different audio formats being used by mods. (no, I'm not talking about wav and mp3.. I'm talking about codecs used to manufacture them)
My point here is to think outside the box. Maybe there is codec issue that nobody is aware of that is causing oblivion-infamous CTDs.
For your first problem when that happens to me it is usually when i first activate the mod. To fix it i exit, deactivate the mod, go in the game save, exit again and reactivate the mod. Loading the save usually causes no problems for me. Its annoying but once I fix it the first time I get no more problems.
And so far I've had 0 ctds (a few blocked) with SE activated and I've played for around 5 straight hours. I dont know why everyone else has so much trouble but my setup is fine with SE on.