I have Logitech G27 Racing Wheel/Pedal set which replaces G25 set. I have set up the set in Game Controller Properties so that the throttle pedal is on Y-Axis, brake pedal is on ZR-Axis, and clutch pedal is on Slider 1 Axis. The throttle and brake pedals are on separate axises. The values on all axises go from -1000 to 1000. I tested combined pedals which are on Y-Axis and it worked. Is it possible to set up the car template so that I can use separate pedals instead of combined pedals?

I suppose you could, but you'll have to do some digging through the template scripts to find the bit which controls the throttle. You'll have to come up with a clever way to differentiate between one pedal and the other, too.