Mystery Overheating problem

I have a 1995 mustang GT that has a mysterious overheating problem. The engine has been built with a bigger Cam and bigger aluminum heads and lighter aluminum pistons. The engine has all new components. It has a 3 row radiator, and all new cooling components and a new temp sensor. And we swapped an automatic transmission out for a 5 speed manual. It overheated before we did all the upgrades and we figured once the build was complete it would solve the overheating problem but it still overheats. The timing has been corrected and is perfect. The valves are set right and it runs and performs great but overheats really quick. At this point I’m at a loss. Like I said all new parts in the cooling system and motor and new transmission. It also has a new driveshaft and a newly built .373 rear end with posy-traction. The fan kicks on a runs when it gets hot and works perfectly. Any ideas??

We’ve ran it without the cap on and we’ve ran it with the the thermostat completely removed. It also blows warm air from the heater so I’m assuming that’s a good sign there are no air pockets. If there was no circulation what would that mean? Could it be an air pocket still? Or would it be the water pump is bad?

We are pulling the motor back out to replace the oil pan and check some gaskets and we are checking the water pump this weekend. Along with trying a different style coolant and seeing if that makes a difference. Probably do all that this weekend and we will see how it turns out.

So I did another test I read about. I took an infrared thermometer and tested the running temperature of each cylinder and found them to be running at drastically different temperatures. Could this be a timing issue, or an issue with the valve setting? Either way we have a guy coming to reset the valves next week but I’m looking for someone else’s take.