Pondering this, at first I thought that Ken's solution of reducing the pcd of both gears proportionately would be the right way to go.
Then I realised that, assuming you are using standard gear cutters, this would mean that both gears would have slightly thinned teeth, which would result in slight excess play (lash) because your cutters are still making normal sized tooth spaces.
So I thought it might be better to make the smaller gear to standard, and reduce the PCD of the larger wheel only. You would then be cutting a standard wheel gap to fit a standard pinion tooth. But then the wheel tooth is still too thin for the pinion gap. There is also the consideration that cutting the pinion small would increase any undercut, but at 39T that should not be problem anyway.
I don't think the resulting tooth thinning of 0.0003" is going to matter all that much. It is enough to make the difference between a fit that runs nicely and one that doesn't want to, so making standard gears and just truncating the tips will not help - it is the flanks that determine the fit, not the tips.
For something closer to perfection, reduce the ODs and nominal PCDs, but cut both sets of teeth slightly shallow to compensate for the thinning. I think I could work out how to calculate by how much.
The late, great, Keith Duckworth would say words to the effect that most problems aren't so simple when examined properly.