am I reading this right? You are coming in on a Sunday night at 4 and I would assume you would go to Jersey for that night. On Monday the 9th are coming into the city and going to do everything on the list? And then come back for a bus out on the 10th in the morning?

If that's the case, you can scratch off the Metropolitan Museum of Art, as they are closed on Mondays. The line at the Empire State can be hours long in the summer. Though it's possible the skip the line feature of the city pass may help, it depends on how many other city pass people are in line.

Also in New York, the speed you walk has little to do with how long it takes to get from point A to point B. You still need to wait for the lights to change on just about every intersection, you can't zip around people if the sidewalks are packed, etc. Get a subway pass, you will cover much more ground in less time.

I don't see how you can possibly do all you have planned in a day unless you literally go in the front door of a museum and walk right out the exit.

Also double check your Megabus departure point, they move them around quite a bit and I don't think they depart from Penn Station any more for Philadelphia. Of course, check again closer to the trip.