I agree with Niles, with the body off you should be able to get some good measurements.
Also, DON'T assume the motor mounts are located correctly on the frame. A 1/4 inch off at the mounts could make 2 inches difference at the end of the pipes. If it does turn out to be the sidepipes, E-M will probably replace them.
You might try taking them off, bolting the two exhaust manifold flanges together and string a line down the length of the joint, extending past the ends of the pipes. I would think (guess) that any measurements taken to the line should be equal on both sides. E-M welds up their own sidepipes and anyone can make mistakes.
Good luck,
Steve