Aftermarket MC brake issues

I went with a small bore MC and larger bore wheel cylinder to maximize the non power drums on the Swinger I am building. I may find myself in the very same boat....
I run the KH 4-piston system with 10x2s on the back, and a 15/16 M/C. The pistons are 1.625 in diameter, and there are 8, so that is a total area of 16.59sq inches. Allowing .015 for knock-back, this comes to .25 cubic inches of volume fluid displacement required in the front. In a 15/16 bore, this requires the M/C piston to move just .265 inch. With a 7/1 pedal ratio, this is just 1.86" of pedal travel. My system works perfect.
To match this with 2 caliper pistons, you would need pistons of 3.25" diameter moving .015 on seal-retraction plus knock-back. You got 3.25s,lol? I think your fronts will be all right.
In the rear you should have plenty