Fans are typically their best at slow speeds. At highway speed there is enough air coming in the grill that the fan is only doing a fraction of the cooling.
A whining sound is frequently a water pump, power steering pump, alternator, etc getting a tight bearing. Just because you have a new water pump, it does not mean it doesn't have a problem, especially if it is a rebuilt pump.
Are you sure it is not a squealing sound? That frequently is a drive belt slipping because one of the above is getting tight and the belt is slipping. A squeal usually show itself on acceleration.
The thermostat housing cracking is common on these. They are a plastic as is the tanks on the factory radiators and age and heat cycling will do that. I had the top tank in the radiator let go. The thermostat housing was next, now that the system could build some more pressure now that a good radiator was in place. I HIGHLY recommend replacing the thermostat housing with the one piece metal aftermarket housing. This is the third 4.0 V6 I have done this to. The previous vehicle has 14 years on the metal housing and still going strong.