1BADAZZGT-How are ya? Still fighting with the car? Here is what we do at the shop when we replace the intake or put new motors in cars.
1. Pour coolant mix into thermostat opening in intake until full.
2. Then fill up resisoir bottle
3. Let it idle to make sure the upper hose hose gets hot.
4. Go drive it and add coolant to the resivoir bottle if needed
The 4.6L is very pickey about air in the system. I had put an intake on a cop car for the recall, filled it up through the resivoir and drove it around the block, I got about 100 ft and the gauge pegged past the L. Rushed back to the dealer, told other mechanic. He said to open take the thermostat housing off, I did and all that came out was STEAM!!! No coolant flowed up due to air!!! I poured coolant into the housing until it was full, re-drove the car-gauge stayed stright in the middle at 190*!
So I always ask people with overheating problems to try to put coolant into the thermostat housing first. Hope this helps and this way you don't have to pay $60-$90 for a flush.