So recently, my animations for just about everything except for the NPC and creature's movements slow down to a crawl.

I open a door, it takes forever to open. I open up a desk, (I have harvest containers mod) it takes forever to open up. I wait for the arena door to lower so that I can have at those minotaurs, but the gate takes forever to lower.
Even particle effects are effected. I hit the wall with something, the dust takes forever to go away. I hit someone, the blood stays on screen for half a second.
It's like, they're lagging or something.

Strangely enough, the NPCs and creatures move normally.

Sounds like the Abomb, You can use bash to fix your saves.

What he means is start Wrye Bash, go to the saves tab, right-click on your save, and select "reapair ABomb", and then answer yes. Should do the trick.