bypass hose and thermostat

I am installing a new sanden shorty compressor to get my factory a/c going again. I was told that if I have an air gap manifold that the bypass hose would need to be eliminated as it would interfere with the retro a/c pump bracket. I have since plugged the intake with a 1" aluminum plug. I then took a 1/2" 14 NPT tap and threaded the inside walls of the bypass port on the aluminum water pump housing. I inserted an aluminum 1/2" pipe plug and all is fine. Now, should I just run the car with no thermostat. Or should I install the EMP Stewart extra performance 300 series thermostat. My auto parts guy said that is what the 300 thermostat is for. If the thermostat (160 degrees) does not open, the water will still pass through rather than take out the motor. I also read to use a thermostat and drill a few holes around the outer perimeter? Anybody have experience with any of these issues?