This happened to me even before TESVAL or SkyBoost on 1.1, 1.2, 1.3 and occasionally on 1.3.10 so this has nothing to do with SkyBoost.
Not really a viable solution, but what I did to solve this (and it has solved it, for now), is start a completely new game. Remove all my savegames, and remove most of the mods that change up too much stuff.
Scripts kick in, there are a few glitches with npc's and grids loading a fraction late. But it's nothing like before.
Way better.
I also sleep for 3 days in a row every few hours of play (resets a lot of cells), use the PCB console command (purge cell buffers), generally don't drop stuff on the ground in exterior cells, and run a mod that clears up dead bodies.
removes a lot of glitch-causing bloat.
I'll come back to all the great mods I had once the constuction set is out, and the mods are more bugtested. Right now a lot of the major mods give me huge issues (not at first, but in the long run).