Thanks for the guidance guys. Will update once i get a day off work to wrench on it again. Work has had me slammed but I am hoping to get a chance this weekend.

 

So it ended up being the VSS. I reinstalled the cats and removed the VSS. The coolant in my reservoir was low, which was causing the codes. After 4-5 drives this weekend only remaining code is the P0500 for the VSS. Ordering that today and will tackle the windows this week.