Thanks for all the input, I'm gonna read through everything you guys posted and start troubleshooting in the morning. Before I came in I did decide to check the battery, and it only has 12.4V when the car is off. Is there a chance the VR is just trying to get my battery up to 12.6+?
I swear the grounds are good. It was charging at 14V with the old ECU at my gauge in the car, but that thing isn't too accurate, and I haven't checked it with the meter in a while, so I don't know if it was happening for a while with the old ECU or not. All I did was put in the chrome box and a new wiring harness, and checked it with the meter to make sure it was all good, and that's when I noticed the 15V when applying throttle.