The cover piece S-503 has some serious wear on the underside but I am going to keep it as is for a while.
FYI, on the left of the picture below is my standard way of repairing nicked screws; its an extremely fine 1/4" square file. Here is the trick to not nicking the screws on an old machine; you must push harder down onto the screw than you are forcing the turn. Sounds simple but the more stuck the screw is the more down force you must apply, any way you can find to push down on the screw VERY hard while turning is going to improve your chances of not slipping.
The new Pinion & Whirl, pretty expensive at around $45 each.
The new Pinion was longer than the old one and so the adjustment instructions in the manual worked very well. There is a screw in the middle of the upper gear that moves the pinion up and down; if it is too far up the cover piece will not seat down and forcing it binds up the whole system; you can feel that the horn won't rotate due to the binding or trys to turn around while stitching.
The alignment of the head is easily done by aligning the marks on the main shaft, this is about half way around the cycle.
It turns out that aligning the whirl to the mark on the horn head S-502 was 180 deg. from where the old one had been. When I tried the machine after assembly it did not stitch at all so I reset the whirl back to where it was originally was and all is fine. More experimentation to come.
Good stitching, I tried a nice groove on the top and it really compresses the two threads together making a very nice looking stitch.