A quick test to determine if the pump is working is to check if the heater warms properly. A defective water pump will not be able to circulate heated coolant through the long heater hose to the heater core.
Are you sure that you have the right pump? If I remember right, the 4.0 is equipped with a reverse rotating water pump. Someone please correct me if I'm mistaken. Reverse rotation pumps should have the letter "R" somewhere on the pump body.
99 Cherokee, 4.0 AW4, NP242
Past Jeeps: 49 Willys, 81 Scrambler, 88 Comanche
Without "data", all you have is an opinion!