We got back from Italy two weeks ago and I miss it... so jealous your big adventure is still to come!
Regarding jet lag, we slept on the plane (courtesy of a sleeping pill) and were functioning 80% the first day, even considering we arrived at 7:55am. If you go to bed early on day 1, I think you will be shocked at how early you will get up day 2. Your body is just confused. But, on the upside you will be raring to go take in Venice that morning!
St. Marco's is amazing. No need to worry about reservations. Read about bag check in the RS book. You have to find the bag check though. Facing the basillica, look to your left towards the building with the digital clock on it. The bag check is in the alley to the right of that building. The bag check is not clearly marked so you have to look for it (it has a grey sign on the wall to the left of the door) (As an aside, if you continue down that alley, turn right on the street ahead and you will see McDonalds, which has Coke with ice at a reasonable price - I was really missing ice by thta point of our trip!!!)
You will then have one hour (but they don't give you an exact time so I think it's an hour-ish) to see San Marco. It is beautiful. Go upstairs to the balcony and to the museum, which we all loved (even my kids). There is a bathroom upstairs, which is HUGE!!! We were happily enthralled with the experience for a little over an hour, when we remembered our bag.
As for Doge's Palace, we loved that, too. Definitely get the Secret Itinerary tour. It's an hour, plus an hour or so to see the rest after its over. Listen to the RS audio before you go, because there are lots of details I missed.
The plaza wasn't as wonderful b/c they are doing construction.
Bell tower was OK. Expensive, bells only go off certain times of day. Not as fun as climbing to the top like we did in other cities.
Have a wonderful time!!