I dont know if you have found a fix to this yet, but i'll give you my 2 cents from helping design a braking system for a mini baja car.
I dont know the exact piston size specs, but i'll make a few assumptions. since you're upgrading from a 2 piston system to a 3 piston system, you are essentially increasing the volume of the piston areas by 1.5 (assuming similar piston sizes), thus requiring more fluid to get the same amount of brake travel. Combine this with the fact that increasing fluid pressure area on the brake piston side while maintaining a constant master cylinder piston area (assuming you dont change master cylinder), you have an increase in your pressure force output vs. pressure force input ratio (example below).
These two effects combined can create a soft feeling in your brakes. you have to move the pedal further to account for the increase in volume on the brake pistons, and the increase in force ratio requires less force to create similar stopping power required for braking.
Simple Brake force calculations: Force/Area = Pressure
Foot Force into Pedal/Area of master cylinder piston = line pressure
Line Pressure * Combined Area of Brake Caliper Pistons = Braking force on Rotor
Braking Force on Rotor * Rotor Radius = Stopping Torque
Stopping Torque/Time = Stopping Power (HP)
there's some unit conversions involved. but basically, your increasing the combined area of brake caliper, thus increasing braking force. to modulate similar braking force (i.e. stopping similar to before), it requires less pedal force input.
