BTW, the heater is making a HUGE difference, rooms warm up 100 times faster and the rooms keep the temperature longer, thus I feel that the heater won't have to run long cycles. Time will tell i guess.
If the blower speed is set at the highest setting it may heat the space up too fast. Usually the motor has 3 speeds (low, medium, high). Does the furnace cycle for a short period or does the air come out the ducts at a fast rate?