Deep cycling a battery ( lights or accessory power on) for many hours can sometimes short a cell within the battery and
even sulfate the cell plates. The battery may have lost reserve voltage even though it has been trickle charged. I would check fluid level( if accessible add only
distilled water if needed) as well as trickle charge every night for a few days. If NG after that your two year old battery may be done.
AutoZone will test your battery for free and even install one for free.
Some better higher end battery chargers have the ability to condition cycle the battery...takes about 24 hours. This breaks down the sulfates from the cell plates and back to the acid fluid.
I have a Black and Decker charger that cost $69 from Wally World.
It does everything from test batt. load to testing the alternater to jump starting and trickle.
But this one also desulfates the battery.
Just some thoughts on your battery situation.
I agree with
bepperb that the the dead battery may have caused the ECM to reset and the ECM must relearn the drivers habits. This may cause erratic shifting at first.
Good luck
LT