First welcome! Everytime I start modifying my car, I am always praying in the corner.
Because it never fails, when a person starts to mod a car (which you have done) you start opening a can of worms for other problems to develop.
First my 96 cobra almost overheats at the redlight, or interstate. But my tach is running at a constant 3 grand with the 4:10 gears. I am going to put a bigger radiator and more flowing radiator next year. That is the first thing you should have done, is put a bigger radiator. Remember, your radiator is made for a stock engine.
Second, I would put in a switch to run the fans constantly. If you car is running properly, you know not missing, running rich, lean, etc. It is got to be either the hoses, air pocket, water pump or fans.
So I would start with the fans running with a manual switch to see if this helps. Secondly, I would drain the antifreeze, and leave the cap off until it the thermastat opens and add accordingly. Thirdly, I would invest in a bigger or more free flowing radiator.
It kills me when people (like my brother for example), will go spend thousands on a bigger bad ass engine, but will put cheap oil and gas in? Dude, throw that stock radiator and water pump away, because it is not stock anymore!
Put just as much effort as you did in the rebuild of the engine and the overheating problem will get it fixed
Good luck,
Rich
Cobra always overheats even with AC off 
