Piririn

Check your load-order. Only time it ever crashed for me at the startup was because i accidentaly messed up my load order. Run BOSS and check if you got any conflicts.

As others have suggested. Try getting yourself killed, let the game reload and then save. Or as soon as you load into the game, Load that save again. (Someone said you need to do this for every session)

Is this with manual saves? or just quicksaves? Im curious because i have been trying to figure out why I sometimes get crashes when quicksaving. Specifically when saving near that lake at Riften (Can anyone else check this?) Dying and then saving+waiting 30 days indoors seemed to fix it, but I'm not confident the issue is gone. My save is about 12mb 200hours into the game.

Dragons killed at "dragon lairs" will not yield new souls once respawned. (Not for me anyways) But if this also happens with random encounter dragons, then I dont know what is causing it.

I dont know if this helps but in regards to choppy Y-axis movement. I managed to solve this by simply running Skyrim in window mode (With borderless window mod) Its the only thing that works for me. If i dont use this method it gets really choppy, especially in indoors areas with spells equiped.