I did the quest in Morthal about the house burning and the little girl ghost, defeated the master vampire. Now when I entered the master vampire's lair, certain areas weren't there, just an open sky void. I payed no attention, just kept at my quest. After all that, the follower for that quest stayed in place. But anyways, after that quest, I can NO LONGER enter the Blue Palace in Solitude, my Solitude house or even explore the swamp around Morthal, without it freezing. The Rift also freezes now.
A few weeks ago, I had a similar problem to the 'open sky void' bug you mentioned. I was in a dwarven dungeon where some ghosts show up (I forget the locations name). After they appeared, a large chunk of the background vanished, showing blue sky. Walking towards it caused me to fall and then I was teleported back to the start of the level. Another problem I had, was when I was swimming in the water outside solutide and a dragon showed up. At the point the dragon appeared, a large square of water vanished. I could swim into it and look down to see the river bed. In both of these cases, I reloaded because I imagined something very bad had gone wrong. Thankfully, after reloading, everything worked fine and I continued to play the game for the next 100 hours and finish the main quests with no problem.
My point is, that there are (thankfully infrequent) bugs in the game which cause things serious things like these to happen. When you see graphical problems like these (i.e. large chunks of background vanishing) I would assume that memory is getting trashed somewhere. When this happens, I always reload a previous save and try again because continuing playing and then saving later, is likely to destroy your game forever. Essentially, if memory is getting trashed, then the information regarding objects and NPC's could also be getting damaged. Saving your game after this happens will save corrupted objects and NPC's states. So, when this happens, there is no way the game is going to be repaired. New patches are unlikely to fix damaged savegames because fixes like this will not be retrospective. Computer games are written with the knowledge that the world is correct and nothing will go wrong. But when it does (because no piece of software is perfect), you will have objects in places that shouldn't be there, and the game has no way of knowing what to do in cases like this. Objects/NPC's can't be reset because of the complications regarding of quest cross-overs.
I realise you are looking for solutions and a way to fix the game you have invested a great deal of time in, and I wish I could help you. I really wish there were solutions to these particular game-wrecking bugs, but the reality is, when problems like these happen, it is highly unlikely that savegames in such a broken state can ever be fixed, due to the random nature of the corrupted data that is now stored in your savegame.
What has worked for me while I play Skyrim, is that if I see any serious graphical problems (like vanishing backgrounds), I immediately reload my last save and continue, because I know that my Xbox memory is likely to have been corrupted due to a bug. So, if I continue playing and save, I am likely to be saving corruption and damaged objects. Future patches will not be able to solve these problems, because patches will only prevent problems from occurring in the first place (because the game is written with the expectation of everything working and being perfect). So, reloading upon encountering any problem has enabled me to play the game with virtually no lockups (only 3 in 250 hours of playing. These happened during loading. I tried again immediately after, and the game worked fine).