Yes, I aligned the pot with the engine running. I installed the pot using the same alignment marks from the old one and left the screws slightly loose. Then I started the car and and watched the voltage reading (pin 2 to ground) while adjusting the alignment. Be careful to rotate the pot VERY slowly or the engine will surge or die.

Also be aware on the M103 that you have to disconnect the fuel pressure regulator to get at the lower right screw on the pot. I just undid the big fuel connection on the top of the regulator (a small amount of fuel will leak out) and also removed the mounting bolt and pushed the regulator aside enough to get the screw out. My car had T10 Torx screws and a Craftman torx screwdriver worked well to reach through all the wires and hoses. When aligning the pot, you have to hook up the fuel line and then disconnect it again to tighten the lower right screw when completed.