Unfortunately yes, you will need dealer assistance at this point. I don't think it is related to your addition of power locks/windows, this sounds like the transponder chip info got erased. Usually this happens due to a magnetic field strong enough, which could be similar to the demagnitizers at the store check out counter. The dealer will have to use the computer to reprogram.
Please update once it resolved, I would like to know how it all went.

 

Update: So the truck has been at the dealer for a couple of days now and all they are saying is I need a new PCM. I took them the PCM from the other truck and they put it in, but they're still getting an invalid key error. I took the second key yesterday to see if it would work, but they didn't have the SKIM module connected so it would work and ended up locking up the second PCM. I hope that after 24 hours it will reset and I'll try the second key again, but I'm feeling extremely defeated. I don't want to pay the dealership $1,600 for a new PCM. I found this site that sells "remanufactured" units. Has anyone had experience with replacing one like this?
http://www.acrautos.com/2006-dodge-d...-computer.html

 

So I shipped my PCM to a company (not the one in my last post) that refurbishes them and they were able to erase the error codes. I plugged it in and it started right away. I reconnected the keyless entry and remote starter and it all works again.

Lesson learned: NEVER take it to the stealership again.