Visual inspection of the tapered holes for the shafts in our flywheels often show shadows of incomplete contact from the last assembly. Often there can be a ridge raised along a keyway, or a burr at the edge of the hole where the nut presses against it, as can be seen here (pic 1).

This one should be scraped before attempting a lap finish. Lapping with a silicon carbide compound relieves the high spots to allow the shafts to be assembled true to their bores. This greatly facilitates final truing of the entire rod and flywheel assembly: (pic 2).

Commonly this is merely done by hand, which requires much patience and good carpal tunnels. Some lapping compound is dabbed upon the shaft and it is spun back and forth in the bore just as one would do with a motor valve.

The better compounds such as Clover brand are difficult to clean up, so often I plug oil gallery holes with paraffin or modeling clay before hand.

The cutting action can be increased by grinding criss-cross grooves in a junk shaft's tapered end to hold the compound better: (pic 3). 

This also tends to prevent annular rings of uneven finish from forming.

Often however, the flywheel tapers have been so distorted as to need a degree of correction. I achieve this quickly by squareing the wheel to the shaft in my lathe, using the tailstock to hold it square as I then throw the chuck back and forth for the lapping motion: (pic 4).

The serrated lapshaft is held in the chuck, and the tailstock uses a common drillplate and a large bronze bushing: (pic 5).

I altered mine to stay fixed together, but tape would do. With the bushing surrounding the protruding shaft, I can apply square pressure gently against the flywheel.

Often I will set the machine on its back gear and power it slow to rough in a particularly bad taper. You can actually see the flywheel rock slightly, lessening until it reaches square. It might take two or three light applications of compound, and several reversals of direction before I can then finish it by rocking the chuck back and forth by hand.

After a scrub, I then polish the taper bore lightly with an aluminum oxide impregnated nylon brush: (pic 6).

This method has tamed some very unruly flywheels, and oddly, it does not seem to sink the tapers significantly.

(Pic 2) Lapped taper.

(Pic 4) Squareing flywheel.

(Pic 5) Bushing on tailstock.

(Pic 6) Shaft and brush.