Skyrim Game Broken! help i really don't want to start over...?

I first noticed a problem with my game going through Ustengrav where you have to use the sprint shout to get through the falling gates. after you get through the gates should trigger and remain open but they did not. I continued regardless. now i'm in one of the black book worlds and when i activate a scrye it lowers the path but does not trigger the moving hallway so I cannot continue... I read that mods can cause trigger to not work so I made sure the recent ones I installed were not on and I still cannot proceed with the game... anyone else have the same issue or know how to fix this?