Put the thermostat back in. If there were three ports for water to come and go from the thermostat, then it's a bypass thermostat and has to be in there.
First thing to check is always a plugged radiator so there's not enough air moving through it. You can put a light on one side and see how much dirt is blocking it, or check the temps of the coolant going to the radiator and coming back when it's overheating, that will usually show not enough temperature drop through the radiator, showing not enough air movement.