Shaft bore location/accuracy for throttle valve

Hi All! Looking for a little help if you don't mind?

I'm trying to bore a throttle valve, roughly 40mm diam. Naturally the shaft centre for the butterfly needs to be bang on the centre of the main bore, at least in one axis.

I'm planning on doing this work on a 3 axis CNC with a positional accuracy/repeatability of about 0.05mm.

Looking for a workflow recommendation for matchin the centrelines of the two bores.

Would you simply flat one side outside the main bore, bore the main bore, then flip the part and zero out on the same face and hope? I'm concerned that with no direct reference to the centre of the main bore, I'm going to struggle to confirm the second centreline intersects, so I'm going to end up with an unrepeatable butterfly profile/hand fettling to fix it.

I'm trying to see if I'm picking off more than I can chew!

Any advice appreciated!

Make a spud to fit in the bore, zero on the centerline of the spud. Bore throttle shaft holes thru from one side. Done.

I'm not sure it needs to be dead on, as the plate is always adjusted on the shaft as the last step. The plate needs enough clearance in the screw holes to do that.

As recently discussed on the other thread, the shaft is offset a little. Usually.