Yes yes. Thanks much for this. I lurked, because I will be critically checking out my 9A soon.
From what I gather so far, chips in the threads stopped the chuck from seating home, but the alignment was better when it was stuck on the chips compared to when cleaned up so that the back face mated.
When we say "runout". Several kinds I read about.
1. There is runout, axial and radial, from when you put a dial indicator to the face and the radius of the chuck itself.
2. There is runout on a drill rod, or some other rod known to be accurately ground, put in the chuck, and you try the dial indicator close to the chuck, and also some inches away.
3. There is runout from a MT3 test bar put into the taper of the spindle. Checked first if you want to diagnose the chuck.
I have to check what might be a typical norm for a SB9A in reasonable condition, but I am pretty sure numbers like 6 thou means it is not yet right. I think the threads are supposed to be regular symmetrical. If you can't put the chuck back plate on in reverse, look hard at the threads of both spindle and chuck. Something is biased to one side.
Short of taking a damaging whack, it might be that using the chuck under load, when it was not fully home, locked up onto chips in the threads, may have had it doing a little high force axial banging wobble, impacting on the chips, and "modifying" the chuck somewhat. A pure speculation on my part - but you got me thinking!