Who replaced the supercharger pump? It's below the heater pump on the 4.2, I went thru the same exact thing replaced the same parts, it ended being the fan, was not running at the lowest speeds and would heat up if not moving over 25 mph or thereabouts. Have you purged the air charger coolant? The system shares the radiator to cool the supercharger, and requires another procedure for purging...

 

My independent mechanic did. Also the fan is working, while idling the fan runs at low speed how it should and even increases speed accordingly. The only thing left is like you said re purging the whole system again. Thanks!

 

make sure the correct pump was replaced, there is a thread, where the top one was replaced by a mechanic(the heater pump). The purge procedure is in the the workshop manual, I believe I needed to get a 17mm hex to open the air charger bolt.
have you purged it from there before?

 

I have found that on the 4.2L the best way is to cycle the engine hot and cold for several days and it works the air out on it's own. Just keep filling the top tank as needed.
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Different version, but same place and size... Fill from there air charger coolant circuit.