I've got a long history with misfires on GPR's, and they all involved either Lyman nipples with CCI caps or Pyrodex. I'm more of a fixer than a complainer, mostly because living so far from sources I have to make things work or quit. Not being a quitter......
I need to get you to define "misfire" a little closer. With the Lyman nipples and CCI caps, the caps would often fail to go off. It turns out the caps weren't seating all the way down. Short solution was to press down hard on the hammer to seat the caps. Once I got rid of the Lyman nipples that issue was solved. They worked fine with Remington caps though, so that was another potential solution. I'd guess that your replacement nipples would have fixed the issue with CCI, but if you're still getting cap failures, try either using a firm press on the hammer to seat the caps better and try Remington caps.
If you're getting pop and no bang, that's the Pyrodex. I'd get half a dozen or so reliable gangs, then a few that were slow to ignite, and finally no bang after the pop. Using a nipple pick after the first 3 or 4 shots with pyrodex solved it, but even better was to change nipples and clean the flame channel several times in long range sessions. Guys turn their noses as those little Allen head cleanout screws, but I loved them.
I think it's important to stick to it and problem solve with the gear and components you have, just so you know how to beat the problems if they occur. I managed to get a supply of black powder, and I've never had a misfire since. Period. But on my personal list of potential "mishaps," my source of real black could dry up at any time. I'm glad I know how to make the pyrodex work now, even if I'd rather not use it!