wilwood brakes

The number of pistons in the caliper doesn't matter. The only thing that matters is the effective area of the caliper piston(s). The stock system has one large piston and it works okay. When you replace the stock caliper with a Wilwood caliper that has four small pistons the total area goes down. When the area goes down the brake force goes down. That means that you have to press harder on the pedal to stop the car.

Don't get hung up on the fact that you have 4 piston calipers rather than 1 piston. If the area is less then the brake force is less. It doesn't matter how many pistons you have, just the amount of area.