2002 Malibu hesitation

I have a 2002 with the 3.1 V6. I was pulling a code P0300 (multiple misfires), so first I replaced the fuel filter, then the spark plug wires (one was cracked), then finally all 3 coils. It's improved, but now it's still hesitating only when the engine is warm. The temp gauge is reading normal, however, I checked the coolant and the tank is empty. Could it possibly be the thermostat? Any ideas?

Find where the coolant is going first, pressure test the system, look for traces in the oil or milky deposits in the valve covers.