After shopping my JD, I notice that the upper loop and Air Raid ramp are harder to hit. The upper flippers don't have the nice alignment pins like the lower ones do. I just put back together my Shadow and fear the same. I tried lining them up with the ball guides best I could.
How do you align your upper flippers? Let them rest against the ball guide behind it? Try making a straight line with the ball guide next to it?