Driving below 3500 RPM in a lower gear isn't going to place any more stress on the trans. I understand your worry, but you will actually put less load on the trans by downshifting into 3rd at whatever speed. It's going to help diagnosis, but suit yourself.
I'll post up a picture of the water pumps and what I am talking about. But if you used a brand new water pump I'd say it's safe to assume that its the better flowing one with the beefier thermostat.
Get an OE thermostat as soon as you can. Something is causing the engine to not cool properly when operated for extended periods of time. I'm thinking thermostat.