At 5500 rpms the engine is working. At 3000 rpms it's dozing and bored and it sounds that way. When it's working, you hear and feel it. You have to get used to the high rpms. Once you've done longer stretches at +90mph you start to realize that that's where the engine is happiest.
Having said that -- if you're not getting that impression maybe something's not as it should be -- but try not to compare it with a newer Yamaha or Honda that will go 130mph in 4th.
When monkey nuts fail, the drive dog fins aren't insulated against the fins in the cup, so the fins whack up against each other and make a clacking noise. In my experience its more pronounced at lower rpms and idle, maybe because it's partially drowned out by engine noise at high rpms, maybe because the faster it spins the more the drive dogs and cup are matched inertially so the force of the whacking becomes insignificant. That's my interpretation -- if it's incorrect I'm sure someone will correct me.
At any rate, pulling in the clutch and throttling down at 80mph will drop the rpms ergo the alternator will spin down, but even with full throttle at freeway speed any alternator noise will likely be covered by road noise. So maybe your best bet is to get yourself a stethoscope and listen to the alternator while throttling up on the center stand in neutral. That's how I was able to locate the cause of then clacking when my alternator was installed improperly -- the nutz had shifted during install and were not seated with the fin between them, which was allowing the drive dog fins and cup fins to contact each other. Stethoscope will help locate internal noises...but i still think your best bet is find an experienced motobricker to ride your brick at 80mph on the highway and give you the qualified skinny. Doesn't sound like your mind will be at ease until you get that frame of reference to work from.
My $0.02...
Van