These parts do NOT need to be programed. Nothing that you're going to do requires any programming so get that out of your head and don't even THINK about going to the stealership again.

See if you can buy the central locking pump including the foam case and the security module with it's mounting bracket and bolt from the guy locally who is parting out his collision damaged Crossfire. Make sure the parts look good (no sign of water damage) and make sure the part numbers match what you removed. Everything is "plug & play".

In the meantime clean up all the wiring and the wire harness connectors using isopropyl rubbing alcohol. Do any of the wires or connectors look burnt or melted? You should also take apart the left side of the trunk so you can clean out the entire lower trunk well area that was flooded. Suggest using "scrubbing bubbles with bleach" and a scrubby sponge.

Do you have water inside your taillights?

Post photos of the trunk well areas when you get them cleaned up and post photos of the wire connectors.

Did you take out the battery and either get it charged up or get a new one?

Let us know when you have the replacement parts in hand.