I was using Caius Cosades house as a storage place and I placed my Gold brand sword and Dragonbone Cuirass and Masque of Clavicus Vile in his house and now I grabbed them back and he tries to kill me. I have no bounty and when I talk to him I open the ~ and "stopcombat" him and then I can again talk to him and he doesnt try to fight me for like 2 seconds. My other problem is that I tried sleeping in a bed in the Skar Inn and got in trouble for sleeping in an owned bed, whatever Ill pay the 5 gold but wait wheres my armor and sword the guard took it!

I dont have an earlier save other than being way way back. Is there anyway to permanently stop him from fighting me and a way to mark the armor and sword as mine and not stolen?

If you use any of the container's in CC's house, that stuff is tagged in game as his. And if you accidentally grab his stuff, well...
And your confiscated materials are in the Evidence trunk in the Buckmoth Legion Fort south of Ald'Ruhn. Usually they have a level 50 lock on them.

Often if you leave a combattant NPC for 72 hours game time (3 days) they will stop fighting you, but they won't be happy. Good Luck.

To stop Caius attacking you, you need to reduce his Fight value as well as using the stopcombat command. Try the following:

setfight 30
stopcombat

To improve his disposition, just type setdisposition followed by whatever value he would have normally, say 40 or 50.

You probably placed stuff in a container, which has him set as the owner.

No skooma for you! :whistling:

most container in homesi n the game are owned.......which is really annoying.

For example when you get given his house, anything you put in the containers get flagged as stolen, then that item for the rest of the game will be taken off you by guards when arrested. It is a really silly and annoying system.

I can't remember - do either the Morrowind Patch Project or the Morrowind Code Patch fix this problem of items being flagged as stolen which aren't, really?

Nope.
The MPP couldn't (since it's just an esm)
And I believe Hrnchamd said that the Code Patch wouldn't be able to fix this either.

just use the jump trick. get on the container and at the apex of your jump open the container. game usually wont register as you stealing.

Inaccurate.
Sometimes you can jump outside of the AI Radius of an NPC with this trick, but the items will still be flagged as stolen by the game engine.

note that i said the game wouldnt register you as stealing and not your items being stolen