b4 i removed all the mods and made a new clean save to know for sure that its the mods' fault, the mods caused a few issues:

1) crashes at random and specific points. on the way back to riverwood from bleakfalls barrow, both b4 i get to riverwood and around the witch's hut. other crashes seem to be random.
2) fps drops that may be random. sometimes i just open the game and the main menu is at 5 fps or lower. this is fixed by restarting the PC but its a temporary and not very fun workaround. fps drops seem to happen mostly indoors, meaning caves and dungeons.
3) that drauger in the coffin b4 you get your first word, he goes out of the coffin too early (just as you get close to it, not after you learn the word) and he is naked. he also does more shouts like disarm.
4) sometimes i find parts of the dungeons gone (no floor, walls, etc) and as i try to walk over the missing floor i am surprisingly fall to the abyss and teleport back to the start of the dungeon.


here is my load order in wrye bash:
http://img826.imageshack.us/img826/8913/85132435.png


so yeah.. it may sound unplayable but the only thing that makes it unplayable are the fps and crash issues.. the missing dungeon stuff only happened once or twice.. and the naked drauger.. well i can live with that tho i would be happy to make it go away.

bump

I'd recommend doing thing in the order I list them:

1) Make sure that all drivers and Directx are up to date.

2) Try deleting your Skyrim and SkyrimPrefs inis and let skyrim generate new ones. Don't change any settings after you do this and try running Skyrim for awhile.

If the above steps don't help then proceed to the below steps:

3) Are your mods up-to-date? You may have a mod that is incompatible with 1.6.89. When you have the empty blue voids or missing parts of a dungeon that usually means you have a mods that has been corrupted by TESVSnip. Any Pre-CK mods? There is a good chance that they were made with TESVSnip.

4) Have you tried starting a new game with all mods uninstalled? Or have you just disabled them? Disabling is not enough as the mods usually comes with scripts, textures, meshes, etc. Your save could be corrupted, so startiing a new game with no mods installed is a good way to test this.