I had the same problem, and at that point the curser turns to the red edit type and the script stops. Now if I manually click on the 3d button the texture will transfer but the script doesn't continue.
I had the same problem. For me it worked to use just Jaycephus' txt file instead of Aurick's in Z2.
Matt, I don't know if I understand your explanation about transparency with alpha, but you said alpha can be a mask to do transparency, but how? i can't do that.