I was hoping you would say thermocouples

A stab in the dark - many Ford 302/351 engines used heads with EGR ports or holes in the exhaust port that allowed air to continue the combustion process, if necessary, in the exhaust system for emissions control. If for instance a head was changed at some point in the engines life, one ended up with those holes and the other didn't, you might have additional air flow right at that port. The heads could even have the same base part number and be a different configuration. Also, those heads often (but not always) had a hump about 1.5" up that exhaust port (again, with or without an EGR hole). I had 2 sets of DO0E heads - one set had the holes and humps, the other didn't - just holes. If that ends up the problem, I'd probably just remove any hump and forget about the temps at the header where I assume you are checking. If you are really worried, possibly check the actual head temps instead. As far as those EGR holes, plug 'em with HT epoxy or just ignore 'em.

Let us know what you find