A few things you've written bring to mind some things I've been going through:
Muffler noise - My muffler has about 20,000 km on it, and is making some noises. Normal running, it sounds normal at this point. Back off the throttle, and there's some minor popping. And when riding around 60 mph and greater, I get a sound out of it best described as the jangles of a tambourine fluttering. (Helps to be wearing an open-ear helmet or no helmet to hear it.) I think it is an internal baffle that has let loose. I will eventually be replacing my muffler. (They are not repairable from a practical standpoint.)
Some of those speed issues you mentioned make me wonder if you have some carburetor jets plugged, although your scenario is not quite the same as mine. Especially the constant changing of max speed and power.
I had lost about 10 mph off of max speed; I took it to a shop and the guy found a wet and oily air filter from blow-back. Replaced that. He also found a few vacuum hose leaks. Fixed that and put it together for a test ride. After that, it was worse! Very slow acceleration, and top speed only about 44 mph. Next, he pulled the carb completely and found plugged jets. (I believe he may have used an ultrasonic cleaner? Don't remember.) After cleaning the carb, I had my original top speed as I recorded when the bike was new (73 mph gps.) Acceleration was way better too.
One last word on fuel conditioners: For about 5 years I was living overseas, and my People 250 was kept in storage here. I rode it for a week or two, twice a year when I came back for visits. I had used Sea Foam for a time, but tried a product called "Sentry" after a while. Definitely had an easier time starting it the first time out of storage with Sentry than I did with Sea Foam.