I am restoring a '64 falcon. Originally it had a 260 with a 2 speed automatic and I converted it to a 302 with a 4 speed.I have recently changed out the 302 for a '65 289.i also put a 4 barrel intake which was originally a 2 barrel. The change over went smooth, but I am having overheating trouble. The motor and car have set for a few years. I have checked thermostat, it has a new water pump and radiator is not plugged. Any ideas?  

If it sat a few years, some of the head/block passages might have crud in them.  I'd reverse flush the engine with a good cooling system flush product and run water through it until it's clear.  It would help to pull the block drain plugs, but that may not be practical with the motor in the car (I typically have to drill those out).  Once clean, pressure test the system and replace the cap with a new one, anywhere between 12 and 16 lbs - whatever it holds in the test.  The t-stat should be at least a 180 - test it on the stove in a pot of water with a meat thermometer before installation.  If pressure doesn't hold, then you've got a leak somewhere that needs fixing.  The radiator needs to be disassembled for rodding to determine if it's not plugged - visual inspection won't do it.  

Also, verify timing - the 289 should like 10~12 initial with 34~36 total.  Slow timing will cause extra heat in the motor.