My c4gf-ae is set up the same

It has CF and A boosters, 48F and 56F jets, no holes into the idle well from the main body.

Ford actually added those holes starting some time in 66, my c6af-f has them from the factory. Not sure just what they do but the c6af-f has very good manners as a result. Looks like Pony redoes the earlier ones and adds similar holes?

On my c4gf-ae that is set up like your carb - I went from 56F to 61F jets in back and it really woke up, gained 1.3mph in the 1/8 mile.

At one point I also went down from 49F to 48F in front - the car went .04 sec slower in the 60 foot. Tells me it wanted to be richer up front, I would try 50F jets next or even 52F to see if it helps. If that works then I would drill out the PVCR's and put the 48F jets back in for best mileage and best power.

Sounds like you need to hunt down some richer jets to try in both primary and secondary, that would be my best guess.