Reinstall the detents in the transmission and make sure you can row through all of the gears before moving forward.

Once everything feels good, reinstall all of the parts that were removed.

Since the battery was disconnected, the car will throw a ton of warnings when it is turned on. Just drive the car around for a little while, stop, turn the ignition off, then turn the car on again and it should all be cleared. If the warnings are still present, repeat those steps.