Just a little explanation 1st, putting the petcock to prime bypasses the on/off feature of the vacuum controlled petcock. When you shut the bike off, also return the petcock to "on". Leaving it in the "prime" setting can lead to overflow issues which you really don't want.
BTW, turning the petcock to prime is the 1st thing to do anytime it acts up (other than electrical issues).
How long are you letting it idle before it stalls out?
It been said that 15 minutes is way too long to sit idle and most only wait a couple of minutes before riding off, doing more or less a rolling warm up.
aftermarket vs. a gutted stock muff... as long as the carb was jetted for the aftermarket, it shouldn't be a problem. Standard answer to anything not stock is... that's the problem. So what "aftermarket" muff do you have?
Personally, I'd ride around locally and if you don't have a problem riding around, your problem is standing still. So it's like when you go to the doc's and you say you get a pain if you stand on one leg... He'll say 'don't do that'. So let me write you a prescription for seafoam and I'll send you a bill for my services