What ignition timing are you running and how are you setting it (jumper in or out)?

Cold start idle is usually more than 1000 RPM, mine is usually 1200 or a bit higher. Maybe the throttle plate is set too far closed. Should be set fully closed then crank the stop screw in 1/4 turn. You said you tested the TPS, was the IDL-E2 setting within spec at idle? If not the engine/ECU will be "running really slow" instead of "idling". They are two different things.