Engine Warmer After Upgrade

simply put, more power output creates more heat output. A minor power increase can typically be controlled within the operating margin of a standard cooling system if in good operating condition. However, at some point the cooling system will need to be upgraded to handle the more powerful engine's heat output. Considering the 64-66 mustang cooling system was nearly inadequate to start with, you may have now exceeded its capability.

Also, with regards to feeling underhood heat, it may just be the headers. Tube headers release more heat than the thick heavy cast iron manifolds that you used previosuly. This might not affect coolant temps, but rather, just produce warmer environment under the hood.

in addition you added the under drive pulley which slows the water pump, which means less coolant is passing over the block, heads, and through the radiator, which means less cooling is taking place.