During normal operation the temperature should be between 80 and 94 degrees C. High ambient temperature and/or high load on the engine could increase the temperature above 94 degrees. Also when driving slowly, there is not much air cooling, so the temperature will increase. The fan clutch will slip less if the coolant temperature is above 90-95 degrees C, so the air flow is increased above 90-95 degrees C.

Your 90-100 degrees C is a bit high. That can be a faulty temperature sensor and/or temperature gauge, they aren't precision instruments. Sensors are prone to fail over time. Can you check the coolant temperature with an other thermometer?

The fact that the bottom part of the radiator is cold would indicate that the thermostat is only partially open and that would imply that the temperature sensor/gauge isn't showing the correct temperature.

If the water pump is new, it is unlikely that it will not pump enough water, unless the paddle wheel isn't tight on the axle (unlikely) or if the drivebelt isn't tight enough. Did the water pump house look good?

Air in the system can happen, although it is my experience it will be pumped out after one or perhaps two drives (showing itself as a reduced coolant level). Did you keep track of how much coolant went into the system? It has to be close to 11 liters (approx. 2.9 gallon), i.e. about 10.5 liters because there is always a bit of residual coolant in the system (mostly in the heater core). Is the coolant level OK?