I figured it out along with the details on testing the sensor leads from the connectors. Turned out the circuit that runs through the pack along each battery was the problem. The only thing that I can assume about its purpose is to let the computer know if a battery exploded or possibly overheated enough to melt the metal strip shrink-wrapped against the sticks. Should be about 20ohms fyi.
Here's the original pack opened up:
http://i.imgur.com/DaovBUp.jpg
And here's the new pack:
http://i.imgur.com/PdlO1Y3.jpg
The problem was with the wire wrapped in red plastic that can be seen cut in the first.
My car doesn't like that circuit apparently.
I would be interested if anybody has any ideas why someone would disable what I believe to be a security feature and why it actually needs it that way.
I also figured out how to test the values coming from the three thermocouplers inside the pack from the outside, if anyone's interested I can label the picture I took of the connector.
I narrowed down the pin on the connector for each of the twelve (I'm assuming since their resistance did change with finger temp) thermocouplers on the end plate but you have to have the top off to test those since they terminate on the stick lug next to them.