a123 Hymotion removal Problems

I have here an 04 Prius with a dead hymotion pack. Figured I'd take out the 200 pound boat anchor. First problems started with the 12v battery. Someone put a highlander group 51 battery in it at some point. It was sitting at 5v and wouldn't do anything until it charged up. Car started fine and drove it home. This is where I started taking the hymotion pack out. After getting the pack out of the car I used the jumper that Hymotion supplies. Car didn't want to turn on. All the lights came on Master Light, CEL about 4 others to the right. Also the hybrid pack (red car) appeared and said problem. Car wouldn't go into drive or reverse. Eventually I get into the dash area where I feel I've disconnected the entire wiring harness for the hymotion and everything is back to what stock should be but nothing changed when putting the key in. I was really hoping to leave the hymotion pack out of it. I put in two code readers and both say no codes. Guys have any idea or direction I should be going in? Thanks