Welcome to the site..
When you flushed/drained the radiator, did you take a look at the bars in the radiator tank for restrictive deposits collected on the bars ends? If the core plugs, you'll tend to see deposits on the bar ends.. When the truck is idling, are both the upper and lower hoses relatively even in temp? A restricted radiator or a bad thermo may cause the lower hose to be cooler or cold if the flow is blocked.. Generally with a wide open thermo, and a healthy radiator you'll be able to see a coolant movement and flow in the tank.. Also, on a throttle snap you may see the radiator level drop slightly as the flow rate increases..
The 4.9 didn't have a lot of headgasket issues, and if bad, may cause system over pressure and/or bubbles in the tank.. Also may blow steam out the tail pipe after a sit/start condition as the cooling system pressure backs the coolant into the cylinder/s..
Could be, and sounds more like the fan clutch is dying and not cooling the radiator with an adequate air flow passing through the radiator until the higher RPM's are made..
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05 F250 C/C FX4 6.0
1969 Firebird Trans Am
2003 Hayabusa GSXR1300
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