The adjustment of the idle screw is not done when the engine is turned off....it is like tuning your guitar - it has to be done by sound!
Get the bike thoroughly warmed up on a about a 10 minute ride....then drop the idle speed down a little bit....and make the adjustment as shown in the following video.
https://www.youtube.com/watch?v=zm5mB3R8UcwIf you can turn the mixture screw in almost all the way and the engine still runs fine - you need a smaller pilot jet.
If you need to turn the screw out more than 2 turns - you need a bigger pilot jet.
Once you get the setting so the engine runs smooth, turn the idle speed back up to 1,000 - 1,100 rpm. You now have the proper idle fuel mixture.
Popping through the exhaust when you close the throttle is not an indication there is anything wrong with your bike....big singles do that. You can turn the mixture screw out an additional 1/4 turn and see if it helps - but don't go much farther or the idle mixture will be too rich. You can learn to hold the throttle open just a tiny bit off fully closed when you shift or are compression braking, and this will cut down on the popping. This is not a fuel injected modern engine....it is a primitive bike that takes a bit of rider participation to operate.....and a bit of learning how to ride the bike smoothly.