I was able to stop by Fry's yesterday and picked up a new transistor. Prior to installation, I tested using the same procedure as before. I was surprised to see exactly the same results as the old transistor, so I retested it too.
Test Pin Old New
E-C 1-2 L L
E-B 1-3 L L
C-E 2-1 L L
C-B 2-3 L L
B-E 3-1 .618 .625
B-C 3-2 .615 .623
I installed the new transistor anyway. After reassembly, the output signal is exactly the same (0.15). The only other components that are left at this point are resistors, diodes, and a few ceramic capacitors. Seems the logic side works, so it must be a power side issue though.