Just quickly looking, the reason T12 isn't getting set is probably the error (extra '=') in this line:
Code:
T12.set=(math.cos(math.radians(theta2)),-math.sin(math.radians(theta2)),0,a1,(math.sin(math.radians(theta2))*math.cos(math.radians(alpha1)),(math.cos(math.radians(theta2))*math.cos(math.radians(alpha1)))),-math.sin(math.radians(alpha1)),(-math.sin(math.radians(alpha1))*d1),(math.sin(math.radians(theta2))*math.sin(math.radians(alpha1))),(math.cos(math.radians(theta2))*math.sin(math.radians(alpha1))),math.cos(math.radians(alpha1)),(math.cos(math.radians(alpha1))*d1),0,0,0,1)