If he sees my character, he runs up, sword drawn and initiates dialogue. Not "you stole that" talk just normal talk. He followed my character all over skyrim and to Windhelm of all places. He won't stop and I'm running out of patience. This character has 50+ hours put into it and I am NOT creating a new one, please any help is greatly appreciated.

reload a previous save?

Tried and still does it.

go to whitetrun, punch a guard, and serve your jail time

Have you tried attacking him? Save your game, attack and defeat him in combat.

Maybe that will reset something.

I accidentally hit one of the Companions fighting the giant outside of Whiterun (at the start of the game). Two of them attacked me, and once I had defeated them, they went back to normal.