So the battery was dead and I hooked up the battery charger and got it started. The trunk does not want to close. After I turn the car off and wait a few minutes it will shut but the handle that comes out barely retracts? The doors are sealing fine . Is there some type of reset I need to do with the trunk since the battery went dead? After I got it closed I started the car again and it poped open again. Any ideas?

Try pulling fuse #9 in trunk wich should reset the close assist system, on earlier cars the handle was driven off the locking pump.