I loaded my save and noticed that about every 5-10 seconds there was a 1 second hitch, this only occurs when i'm in an indoor location. After playing around my house I noticed that one shelf could not be hammered, I cannot burn it, I cannot remove it with console commands. i'm not sure it's causing the hitch in the game but both things started to happen at the same time.
I should also point out if i make a new game I don't have this problem, only on these saves.
Added my save as well.