I've been having some of these same issues and decided to post in this thread.
My 2002 1600 has a distinct pop/flaring coming from the rear exhaust pipe. The front cylinder exhaust sounds regular and subtle as I would expect both to sound. I have placed my hand softly over the exhaust pipes one at a time and feel/hear a distinct difference. The pop/flaring sound seems to hit at every other combustion cycle on the rear cylinder only. When I ride, I can hear the distinct sound in the exhaust, hear a plunking sound coming from the engine that hits in unison with the exhaust sound, and a very heavy vibration that gets worse as the engine gets warmer. I checked the compression and it is within specs. I installed new intake O rings on the intake which seemed to improve greatly. The vibration almost disappeared, but the popping/flaring remained. My brother-in-law rode it 10 minutes and said it ran better than when he had it --- until the next day when I drove it 25 minutes to work. As it heated up, the vibration returned and got worse with heating. (I'm not sure, but the rear cylinder seems to get hot, although I did not compare with front.)I removed the intake again and applied high-heat silicone around the flanges, re-installed it and let it sit for 24 hours. I took it out and the noises and vibrations were evident from the start. I was going to swap the coils and plug wires to see if there is any change, but found that the wires were attached to the coils and did not want to pull them apart. I'm thinking of getting Nemesis coils and wires in hope that they would resolve this, but don't want to be disappointed if this is not cleared up after spending more $ .
I have been considering valve timing, valve damage or lash and do not know how one cylinder can be hitting harder every other combustion cycle. The popping sound is like one would expect from and exhaust with no baffles installed(which I have). I have been a backyard mechanic all my life and have spent countless hours on gas and diesel engines and am confused over this one. It is a really nice scoot, but I can't ride even 50 miles on it. I want to clear up this problem and am ready to pop off the valve cover on the rear.

Sorry for being long-winded , but any direction or help would be GREATLY appreciated.

Rayjay