I decided to use the quartering jig to hold onto the crankpins while the epoxy holding them in place cured. The theory was that regardless of where the actual holes in the wheels wound up, the vital metric was the distance between wheel centre and the crankpin itself.
So, I gave the quartering jig bosses a quick spritz with mold release and dropped the crankpins into the crankpin holes. I then spread a tiny amount of epoxy around the upper edge of the crankpin, and pressed the wheel down. I also placed a tiny drop of epoxy on the back of the wheel. The hardest part was resisting the urge to pick it up to see how things were going before the epoxy cured.
It seems to have worked! At least, no wheels became permanently affixed to the quartering jig, and all the crankpins appear to be straight and the same distance from the axle. Even the wrecked driver looks usable, although a little carving and filling will be required.
My one mistake was to incorporate a spacer into the rear crankpins (the spacer accommodates the main rod, which is in-board of the connecting rod). This spacer, required a corresponding divot in the quartering jig, and that makes the jig less firm when it comes to holding the forward axle. I should have made a little sleeve instead.
Pembroke:87 
Your work is fantastic!!!! I was wandering do you think the way you build your drivers would work in a larger scale like 1/32 G scale with the plastic centers. I would love to scratch build NYC 999 in 1/32 scale but as you well know drivers seem to always be a sticking point in a project.
Best Regards
Robert
Definitely. You would need a much bigger lathe to be able to push a form tool around the 2 1/4” diameter wheels. The wheel centres here are actually steel with a plastic overlay, which makes them more robust than plastic, and I think that would be a benefit in the larger scale too. Let me know how you get on!