After chasing down security and radio gremlins I found a few things to be out of the ordinary and I cannot ID them. Of the attached pics, what's stock? and whats everything else. I know the clear box interacts with the VATS

 

Does the car have a aftermarket remote start or security system?

 

After chasing down my stereo it turns out this is all part of an alarm system that a PO took half of it out. Not knowing this car too well I was hesitant to rip wires out but I got ballsy and did it anyway, Problem solved