Hello and happy riding.
1. I notice a hissing sound on right side of bike sound like it is around air box.The sound pulsates like one thousand one..one thousand two...,etc.Not real loud but concerns me.I practically saturated the bike with propane to check for vacuum leak.Nothing,idled fine.
Unless it's affecting the bike, just go out and ride. Meet up with someone else and hear how their bike sounds. Adding your location in your profile would make this easier, getting local help or meet ups.
2.bike is a bit rough off bottom when accelerate,not bad ,but it may have been sitting for awhile,so seafoam.
Berrymans B-12 would be better. 1/2 can in half a tank of fresh fuel. Run the bike in the RPM range that you think is the problem.
Mine is running fine, but I'm going for a 500 mile ride tomorrow, and just dumped a 1/2 can in my IS full tank. Not having troubles at all, but a good time to run it through the carbs.
3.noticed a bit of engine noise on left side ,like a small clunking,but seems to pop up when engine warm.Think it is at the back of motor near the shaft connection to drive shaft.My notes with bike show that the universal has been replaced.
I would research for u-joint, pinion cup, and rear roller bearing symptoms.
While you're at it, look up hydro lock and rear end maintenance. Something you want to know about, and something you want to make sure is done.