I'm pretty sure you know all this, but I will try and remind you in case you forgot.
If you remove the thermostat and run the engine with the rad cap off if you have any compression coming into the cooling syst you should see the bubbles come up to the top of the rad.
The belt routing can change the direction the water pump turns , make sure it is routed correctly.
I know the engine you installed was flushed and not full of stuff that could limit circulation, right?
Sometimes fan blades get installed backwards and don't remove enough heat.
By the time you read this stuff you probably will have it fixed !

 

I did get it fixed and what it needed was a new fan clutch and water pump. To answer Haha power's questions the truck is a 96 and the engine came out of an 89 I used all the parts off of the 96 engine so that it would still run and hook up the same as it did when I took out the 96 engine