Charging

If you haven't done it yet, check the alternator drive belt and associated pulley surfaces. If there is slippage, your alternator will not charge the battery. As always, with these old horses, verify that all of your grounds are good.
Cheers!
Ron

Double check your fusible links at the starter solonoid. If one of them is burned, the charging system will not work. I'm assuming the control box you're referring to is the voltage regulator. Trace the wiring between the regulator and the alternator as well. I've had to run new wiring between the two before especially on the early iron. I have a 68 Mustang myself and had the same issue before and decided to use a Chevy 1 wire alternator instead. Definitely a much more simple set up being that the regulator is built in. It looks stock and I was able to clean up excess wiring in the engine bay for a cleaner look. Let me know if you'd like step by step installation of the Chevy alternator. It's very simple. My email address is proracer88@live.com. I've had problems in the past receiving emails so I may need yours so I can get you the information. Try this address as well tiqautoperformance@live.com. I'm really big into the early Mustangs. Mine runs a 331 stroker with a 4400 converter/C-4 reverse pattern trans. with an 8in. rear, 4.11 gears. Goes 11.81 @ 114 on pump gas and I drive it all over the place. Never gets over 170 degrees on a really hot day either.