At this point all you can do is stick a garden hose in the top of the motor somewhere, run it, and let the water run out the bottom to flush. You can pull one of the heater hoses off and run water into it so that it will also flush the heater core.
I would say a 180* T-stat would be a good choice. I personally run a 160 all the time for various reasons. Make sure the new water pump is a cast impeller type and, like crazy's link, make sure you set the correct gap for optimum flow. Make sure you replace any divider plates that are rusted through and replace the rubber collars that mate to the backside of the plates. If it wasn't overheating before I wouldn't mess with it too much, Pontiacs seem to be kind of touchy about their coolant systems.