Your assuming that the surface you are sitting on has been machined perpendicular to the bore. If it were mine, I would check the SJ in multiple positions mounted on the shaft, while recording TIR each time. That is real info you can use. You should be able to tack it within 0.020" if you are eyeing it while spinning on the box.
You're right,
Mounted to the new shaft and taking measurements to the deck is real world and best. I had done exactly that when troubleshooting the first time, and have video/pictures of that too. But, I found the bad gearbox and seal, I assumed that's why the jumper measurements were off. When the replacement gearbox arrived, I mounted, and could no longer clunk the jumper back and forth, and no oil was leaking, which I was very happy about, but the run out appeared exactly the same, and the blade tips still resting way out from one another, and had the same aggressive wobble while running. So in frustration, I removed the blades and jumper, again.
So, I just whipped up a benchtop test. The 2 photos I posted at the beginning, are screen shots of a video which would inspire a bit more confidence in the method than pictures. This method depends on the jumper pinion collar top being perpendicular with its shaft bore, which it should be. Spinning the jumper 180 degrees in place, collar down and flat, taking a measurement from the exact same reference point on the table, and nothing else changing, I can determine the 1/4" difference from hole to hole.
I'm not really concerned with any other points on the jumper but the blade pin holes at the ends of the blade bar.
Thanks for discussions and comments so far, all.