It's interchangeable, no problem. Make sure though you remap your ECU so your engine knows what to do with the extra amount of air and also make sure your car can breath on the exhaust end
AFAIK you need to machine the b16b pr3 piston to make them work with b16a rods. something like 1mm machined off either side to make the piston accept rod.
I believe it was 1mm off each side of the rod, and b16b piston is not pr3, its pct.
Do your research before even thinking about anythink. It sounds like your quite new to the game. A good final drive and lightweight flywheel will work wonders on any na civic. Pm Mfactory for more technical info .