Remember when I told you that where you place a comma sometimes indicates what part of a sentence can be left out without changing the basic meaning? If you leave out except for John, what does this sentence say?
Yeah. That’s why there shouldn’t be a comma after everything.
Also, who just woke up… explains/”renames” John, so you do need a comma after John.
Gravity works well for everyone and everything except John, who just woke up on the ceiling of his apartment.