I'm not sure if you have an issue to be honest. I'm running the PR60/60 combo with the stock master cylinder and booster. The pedal feel isn't great, and you can push it to the floor if you try. I've never actually had a problem stopping though, including lots of high speed road miles and several offroad trips.
I have the Mopar big brake booster and master cylinder but haven't installed it. Before I figured out how to relocate 3 solenoids, an ARB twin, and all of the other stuff I have under the hood I got used to the pedal feel. It's on the to do list, but it's a not a high priority. I've heard from several people that the pedal feel didn't get better after installing the bigger booster and master cylinder, and my local dealer probably wouldn't be able to bleed the system correctly if I get air the system while installing the booster and master cylinder.
Are you having issues stopping? After bleeding it myself several times, I took it to the dealer for a pressure bleed. It still has a lot more pedal throw than it did before the 60's, but it stops fine. It was something I was really concerned with at first, but was the smallest issue I had with my PR60s and I forgot about the difference in feel and pedal throw over time.