2) Can you maybe close its lid? I think the physics is only disabled if you close the crate ^^
And the guards you had are spawned in by default, they did not originate from your purchase
5-6) I feel those are closely related, something about the horse and exiting it on a slope does mess up your character view (which only seems to affect the P-character sheet menu as of now, and some collision checks)
If your character is messed up, you can use my fixer, the latest version supports resetting the player position / rotation, which does fix this issue - not the horse waggon though if it is going nuts - if people ask for it I might be able to hack this in this week
The program will do backups of your save, but to be sure you can also backup your save file - good luck!