I have a 2001 Nissan Frontier Crew Cab XE with a V6 (without the supercharger). I bought it on Halloween night (no comments, please) with only 42,000 miles. It now has 112,000 miles on it. I moved from Georgia to Kentucky and heard that I needed to have the cooling system flushed/filled to prevent it from freezing in the winter time. I then noticed that it would periodically "overheat." The temperature gauge would climb up to the line just below the "H" and then I would turn on the heater. I read online about a "bleeder valve" on top of the intake manifold. I loosened it, squeezed the radiator hoses to get all of the air out and then tightened the bleeder valve. I then let it run until the thermostat opened, revved it up to 3,000 to let all of the coolant flow. Now, at various time with no specific reason, it will run fine and then just "decide" to overheat. I can drive it on the interstate for fifteen minutes, park it in front of my house and then have to "tack it up to 3,000" just to get it cool. I've changed the thermostat and had the water pump tested. Neither of them are faulty. My mechanic vacuumed out all of the air from the system with a special tool the dealer recommends using and it still does the same thing. What's going on with this vehicle?

Here's what I would do:

. Replace the radiator. Tap water reacts with antifreeze to form phosphate scale, which frequently blocks passages in the radiator and heater core.

. Replace the coolant with a 50/50 mixture of the recommended antifreeze and distilled water. Read the Owner's Manual on how to refill the cooling system with antifreeze. It may be that you keep adding coolant to the radiator, until it comes out of the opened bleeder bolt--I suspect this is your procedure but it should be confirmed. It may also be that you turn the ignition switch to ON and rotate the heat control knob to high, which opens the valve in the heater control unit. The procedure varies from vehicle-to-vehicle. Failure to do it right can quickly lead to the vehicle overheating, blowing the head gasket, and warping the head and destroying the valves. Several weeks ago I helped rebuild a 2002 Civic LX to which this happened. The repair estimate was $3,200, which the lady could not afford. If the tech had only read the Owner's Manual on how to properly refill the cooling system, the engine would not have overheated and blown the head gasket.

. Verify that the radiator fan operates properly--check fuses; Engine Coolant Temperature (ECT) Switch, not the ECT Sensor; and radiator fan relay. The cooling fan not operating properly is one of the most common reasons engines overheat. If the coolant is low and/or there's air in the system, the ECT Switch may not turn the radiator fan on.

I have a 2000 Frontier with 103,000 miles and have never changed the coolant because I figured after reading the procedures that I would probably screw it up, and I read the procedures in a popular repair manual available at auto supply houses (not sure if it is proper to say the name so I won't but it is about the only repair manuals I ever see in those stores). The book I have is for Frontiers from 1998 through 2001. The procedures seem pretty complex and I think as greasemonkey said you need to make certain you have the correct procedure. I had tried to purchase the service manuals for mine shortly after I bought it new and was advised that it had been computerized and books were no longer prepared so I bought the auto supply house manuals.
As greasemonkey has said-- the first thing they mention is contaminants and they do mention that cleaners are available for this purpose but I don't know how effective they are.
Something I notice in stumbling through all those procedures is that there is one procedure for 4cyl/3.3LV6's and another procedure for 3.5L's.
Also procedures for removing drain plugs during draining operation which you didn't mention.
There are two relief valves for the 3.5L.
For 4 cyl and 3.3- the thermostat is removed and housing with no thermostat reinstalled before flushing. Steps for thermostat removal do not apply to the 3.5L, if I am reading it correctly (there are some ambiguities in the procedures).
There are ten steps described for just the refilling process- too much for me to list here.
After reading the procedures for about the last hour and trying to write this response, I am still not sure if I will try changing my own but I think that the chances of getting it right without a manual are pretty slim.
I don't know if any of this helps you or not but even if it doesn't I got a little bit out of the exercise myself-- and maybe greasemonkey will see something that strikes him as being key to the problem.