Thanks for the replies! I got some help from the friendly folks at
http://cambridgehackspace.com/.
The first thing we did was get out the multimeter and confirm that we are getting power on the left hand pad. Nice clean 5v coming through there. I also double checked the jumpers on the sides of the trrs connectors. As far as I can tell they are correct. I'll post pictures tomorrow.
The next thing that they had me do was follow the tracks on the pcb diagram and make sure that all of the pins that were supposed to be connected to each other are. I think the goal was to make sure that none of the tracks had been damaged by the heat and removing the first MCP. Once again everything was fine, buzzer on every one.
The only thing that I did find that was odd was the voltage drop across the keys. On the right hand pad which works, there was a voltage drop of ~50mv between the two pins on each key. On the left hand pad which doesn't, the voltage drop was ~5mv. Not really a diagnosis, but another data point. At that point, I also double checked the resistors and confirmed that they were the right ones.
I'll get another stab at it next week. Someone is going to bring in an oscilloscope, and apparently they have something called a bus pirate? We'll use that to check the output from the MCP to the teensy.
Any other thoughts or suggestions? Did the key voltage difference sound familiar to anyone?