New Battery in Ford Fusion hybrid - still won't start

The battery went dead on my 2013 Ford Fusion Hybrid after I left the lights on.
I tried jumping it and the lights went on--and error lights started cycling but I
couldn't depress the gas pedal and start it like normal. Te juice soon died. I
tried a battery recharger for many hours (12) but nothing. So... I bought a new
battery and installed it: the electrics go on, and I can see a number of error
lights cycling--but a Ford guy that was to be expected. He said I would
probably need to take it to a Ford service to redo the software, but that the car
should really start. But nope: the gas pedal is form and won't go down. Any
thoughts?