The "otehr side" of the cooling system is the heat generator. If the engine was properly rebuilt, they should have cleaned out the cooling jackets. There typically is a ton or casting sand left in there from the factory install. It sticks, and doesnt get washed out, and then fills the bottom of the water jackets as the engien is run. The places heat is supposed to get into the cooling system is the cylinders and chamber areas of the heads. Which is why the timing curve and compression ratio are important. Either can drive the amount of heat going into the system up. As can pistons that are too tight, adn rings that are too tight and butt. Do you have an HV oil pump? If so, they are also a HUGE contributor to heat. Because they are trying to compress a liquid in a confined space as soon as you get off idle... That creates heat in the 2nd cooling system the egnien has... the oil. If you have 75psi or higher after 2K rpm, it's too much and that HV pump is bypassing trying to pump too much oil through it. That adds a LOT of heat.
Edit: if it was bored .040 or .060 over, it also could be runing with one or two thinner cylinder walls... which also add heat.
You have all the cooling area you need. I think it's an engine related issue at this point.