MAER,
I think a standard thermostat is designed to flow as much or more than would be required for the engine. Drilling a 1/8" hole in the thermostat flange would allow any trapped air to pass and guarantee that the thermostat was surrounded by water.
A good radiator hose has lots of strength. Lower hoses sometimes come with internal springs, but I don't know about upper hoses, as they are on the discharge side of the pump. If yours feels soft and spongy, it might need to be replaced.
Jegs does show a high output pump, but you would have had to order it specifically...and you would probably would have known. I would do the thermostat, maybe a new top hose, check the radiator cap, and give it a try. Running it with no thermostat would be counter productive.
Stuart