Double check your keyboard assignments. Now, if you're not having issues with other activation, you're most likely not going to find anything. But at least you should check that just to be sure. And other than that - I don't know, never had anything like that happen. Hopefully someone with more knowledge will be along to help you out.
As far as I know, there is no way to fix a corrupt save file. Not trying to be presumptuous but it sounds like the kind of thing that happens when uninstalling certain mods mid-game. Not that this will help you but I once uninstalled a mod which corrupted my game 40 or 50 hours after the fact. Sometimes these things can sneak up on you.
If you have not uninstalled any modules, you can use xEdit to find out which mods are overwriting each other and possibly locate the culprit. However, even finding the issue will not correct your current save if it is corrupt.
So, a couple things...
One, I have now sort of fixed on of the problems: not being able to progress through the quest. I used console commands to cheat my way out of talking to Harkon, and boom, on with the rest of the quest. Thing is, I still can't talk to Serana. Seeing as she is now my follower for this quest, not being able to interact with her is a pretty big problem.
Two, there's more to this whole not-being-able-to-interact-with-NPCs thing. With Serana, I started crouching/standing up rapidly while spamming the 'E' button, and it sort of worked. There was no menu that popped up for dialogue, but it did put me in command-my-follower-to-do-sh*t mode. I could tell her to wait places and do things. I didn't choose this option anywhere nor did any notification for me to talk to her show up. This is reeeeally weird.
Any ideas would help, thanks!