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I forgot if you had a cobra or GT. If you have a GT then when you put the motor back together did you fill the motor up with coolant through the thermostat housing in the intake until it is full, then put the thermostat on and fill the rest up through the resivoir.
If this is no help or if you have a cobra let me know.
 

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Take the thermostat housing off and check under the thermostat and see there is coolant in there, also fill it with a 50/50 mix until its full. Then put the thermostat and housing back on, fire up the car turn the heater on floor low and let it idle for a while, check the temp gauge and feel the upper rad hose to see if it gets hot and the heater gets hot. If those both get hot then that would rule out any trapped air in the system and the thermostat staying closed. I would then have to suspect the fan or the water pump for poor flow or blockage.
 

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SO fill out this check list for me;

1. Upper radiator hose gets hot?

2. How old is thermostat?

3. Make sure fan works by turning A/C on?

Let me know
 

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After all that pressure that the blower put on the cooling system I would have replaced the thermostat. It may have gotten damaged, they aren't exactly a high quality part. Throw one in and see what happens!
 

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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.
 
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