First, if you use circumference (dia x pi), after you do you calculations, you have to divide by pi to get the dia for clearance. It makes no difference, just use dia.
using a 4" bore, if we use pbf's expansion rates, we get .003068" for the cyl and .006543 for the piston. Off hand, I don't know the expansion rate of 2618 aluminum, used in pistons but, if it's the same rate that pbf offers for aluminum then you would use ~.0055 clearance and the piston would be 3.9945.
Cyl will be 4.003068 and the piston 4.00104, when both are heated 130°.
I believe the expansion rate, for 2618 is less than the .0000126 used.