Your misunderstanding. Letting an air cooled bike idle for too,long without airflow is bad for the bike but doesn’t make it smoke like your bike was. But because it was overheated it made the smoking a lot worse....The only reason your bike was smoking was for the previously mentioned reasons , either tappet caps, valve cover , head gasket, unrinsed gunk, or internal cylinder issues escaping through the wrongly assembled exhaust components. If i overheat my 550, it will not smoke like yours because I have no leaks or cleaner laying on the engine, or mis assembled exhaust parts....
It’s not smoking now so that’s good, you must not have rinsed the gunk off good enough.
Your manual will tell you the proper idle speed. You say your new at this so all four carbs need to be balanced.