One thing you can do is di away from zss to avoid up air strings after dthrow(to which zss can respond with fairs, so mix up your di)
Also, don't punish with ddd dash attack, it's too slow.
As you found out, don't hold a move and be stationary.
At times you can challenge flip kick. Like with greninja, you can use your disjointed fair to intercept the flip or up smash to disrupt it. (As a note of caution, this is dangerous, you could trade, but not in your favor, our you can hope he doesn't activate the kick and you can catch him off guard)
You can also roll or spot dodge. Dodging the stomp will force zss into the bounce off animation which has lots of lag, and of he kicks, you can punish the landing lag.
Ps. Nice dunk
Marios head is invincible during up smash, so you can throw that out whenever he flip jumps.