I would syncronize the carbs, assuming all your other tune up stuff is in good shape. Even if you did sync them, I would do it again before changing pilots. Are you running an ignition advancer? The bike idles smoother at stock advance. Are all you intake boot clamps snug and the vacuum plugs snug in place, no intake air leaks right? All vacuum tubes are good. Check them all, any fresh air getting in between the carbs and the block will cause irregular idle.
If, after you are sure that you have good carb balance, you are still not happy, call Ivan. He certainly knows his stuff and has a good reputation for helping his customers. He has taken calls from me, and he doesn't know me from Adam.
My guess is that if your bike runs like a dream except for idle, changing out the pilots will degrade performance.
Steve