Made a jig to align the spokes, and then, with the spigot fitted and a slip gauge under the rim, marked through the counterbored holes onto the second flywheel with a drill:

Then centre-punched & drilled:

Countersunk slightly:

and tapped M4:

All fitted together nicely (dry):

I then put the assembly in the lathe between centres, and checked runout.
Radial runout on both wheels was a couple of thou, but axial runout was 0.018″, and gave a visible wobble.
From this I assume the two wheels are not co-axial – this seemed to be confirmed when I could feel a slight step at the join line on one side, but smooth on the opposite side.
This may not be surprising since despite re-machining the spigot to give a better fit, I can still very slightly rock the two wheels against each other. I don’t think I can get the spigot a tight fit on both wheels due to the bores being very slightly different. I tried a dodgy method of centre-punching around th espigot to get a tigher fit, but obviously that didn’t work too well.
I suppose I can try to correct this by feel on the step of the rim to get them more co-axial, but it’s a bit hit-and-miss- especially when I finally assemble with JB Weld.
Anyway, it is what it is (which isn’t a disaster by any means), I will just have to get it as good as I can I guess.