Boxnife that's one lovely old bike you have there, and you have improved her running considerably since your first video.
Do you know how old the air filter is on her? It makes a huge difference to the running as part of the equation is spark-compression-air-fuel, any one of these can let you down
If the air cleaner hasn't been changed since the dawn of time or you have no idea of it's age I'd definately replace it.
Not much you can do to improve the bike after that, as the other guys suggested ride it and maybe clear that possibly jammed ring, if it's a busted ring
then you face a top end teardown which isn't a major considering your level of competence with mechanics.
You asked before if the top end can be done leaving the engine in the frame, for most of these SOHC 4'S the answer is yes so can't see the 550 being different.
Good luck and welcome to the site.......Hush.