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I have a hand vacuum pump that I use for bleeding the brakes and testing vacuum-powered components on the vehicle. I bought it at Al's, before it became Schuck's, before it became O'Riely's... anyway, it wasn't expensive and it has a guage. You can try to operate the heater water flow valve with a hand pump and see how much vacuum it takes to trip it. You can then hook up the pump to your vacuum line with the engine running and read how much vacuum you have. I did this to my truck and fixed the heater, the brake-boost, the 4X4-shift-on-the-fly, and I think the turbo... but I'm still learning my truck.
Sounds like air pockets in the coolant passages. Have you run it up hard to redline at all? Sometime high rpms help push out the air, other times it takes steep inclines to help it out.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.