I run a '70 Challenger with later disc spindles... probably similar to your setup. Also upgraded discs with Cobra calipers. I run 13" rotors front... I don't think you said what size you run.

Anyhow, the Cobra calipers have significantly smaller piston area vs Mopar OE single piston discs. They need more line pressure. I started with a 9" OE single booster and OE spec disc/drum master. Brakes were OK but not 100%. Granny brakes? It took a Dr Diff 15/16" master and dual 8" booster to get to 100%.

I wonder if you just need more line pressure than your current setup can provide?