My 1999 +8 (which is Hotwire not Flapper EFi) has the water temperature sensor for the gauge in the radiator, not the engine. If you removed the radiator to install the new pump have you checked the connections with the electrics. One set is the otter switch which signals the need for the fan , and the other is the temperature gauge. One is at the top of the radiator , the other at the bottom.
I agree that the ecu probably gets its reading from elsewhere (someone like Mike Smith (Teknome on here) is the guru on the electronics, I hope he will be along soon to advise.
