Watch the manifold vacuum and see what it is before and after you shift, if it doesn't drop enough when you shift you will need to change the springs in the power pistons to get more fuel.
What I'm trying to say is you need more fuel to compensate the air, 2 4bbls wide open will need a lot of fuel when the engine slows down and the air going through the carbs slows down and doesn't pull as much fuel.
I had the same problem it ran great with 4.88 gears then put 3.91 and ran it on the street I had to reset the carbs because it had a lean bog because it had more load for a longer time.