Your expert guidance is requested.

It was my third time visiting Venice before I realized that getting up and going out at 7am was totally worth it. Head to Rialto and st marks square. Go look at the bridge of sighs without fighting elbows and selfie sticks. By 10am, they are full of tourists and day trippers...that's when you go off road so to speak and visit the quieter parts of Venice. Aka...anywhere about five min away from the Rialto to SMS gauntlet. Even one morning head out that early (hopefully you are staying in Venice proper...we'd go out for an hour and a half then go back to our accoms for breakfast).

Also, try to eat away from the Rialto bridge area and the grand canal area just beyond SMS. The food may be ok, but is way overpriced.

If you want to go up in one of the bell towers, may I humbly suggest San Giorgio, across the lagoon by a short vaporetto ride from st marks. We had no lineup to speak of (first trip we did San Marco bell tower and waited a good 30-45 min to get up). And awesome views of st marks and the bridge of sighs and all of Venice. And cheaper. If you do decide you want to do San Marco, and can somehow time it to be up there on the hour when the bells ring, it was really awesome (and loud) and a fav memory.

I'd also recommend the vaporetto pass. The individual rides are pretty pricey and the passes just make it easy to hop on (make sure you scan first!).

(Can you tell I love Venice?).

What Nicole said.... watch the sunrise in Venice as often as you can... it is simply magic:) I love Venice to, but I would not feel that way if I had only seen it with hordes of tourists in the sweltering mid day:)

You can probably just sign up for a winery tour from your hotel in Siena for the following day. I have done this a few times, but I left from Firenze, but I assume they would have some leaving from Siena.
Have a great honeymoon!

On one of my trips to Siena I was there with friends during the lead-up to the Palio. We left the day before. It was a really fun time to be there. It's not a tourist event -- the residents take it extremely seriously. It was noisy as people from the various neighborhoods paraded and sang all over town day AND night! Streets were closed for block parties, and while we weren't invited to join in (and didn't expect to be), it was great just watching all the parties and celebrations.
For views of the countryside, find your way out of the Campo to the right (as you are standing at the top looking down.) I remember a wonderful meal at one of restaurants located outside the buildings that line the Campo, not within the Campo itself, if that makes any sense.
Have fun!

Oh yes, the best times in Venice are dawn and very late. The Grand Canal before dawn in the misty light, then watch sunrise over the lagoon. Ride the vaporetto down the Grand Canal again at 11 p.m., with hardly any traffic on the water and the beautiful buildings illuminated.

My 2 cents on Vernazza (been there 5 times!). The other towns are all about 5 min. apart by train, so try to visit each if you can.

Best restaurant, IMO, is Il Pirata. Up a short hill above the train station, 5 min. walk. Great breakfasts, pastries, and just as great dinners. Run by 2 brothers who are very friendly and funny!

On the bottom side of the train station is Blue Marlin, a great bar for snacks, drinks, people watching as the tourists come off of the train, and early evening fun. When they close, and everyone else closes, walk down towards the harbor (5 min) to The Bar. Only place open and all the locals hang out till late. Again, very friendly people.

In Riomaggiore, I would recommend La Conchiglia for lunch as they have one of the best views and lunch type foods. It is down by the water, but up high so you get the view. Easy to find, down the main street.

For hiking, the trail from Vernazza to Monterosso is one of the more popular. Start early as it gets crowded. There are a LOT of stairs on the Monterosso end so it depends if you want to walk down the stairs (coming from Vernazza at the end) or walk up the stairs (starting in Monterosso) to Vernazza.

You will enjoy your honeymoon, no matter what! Italy is great!

You are probably leaving in a few weeks, but if you can swing it to spend the night of the Palio in Siena, I would. Yes, it's crowded and you have to watch out for pickpockets, but it was one of the coolest things I have done in all of Europe. If you have been to a MLB game, the crowds aren't much different.
Il Pirata is a nice breakfast place and the two brothers are entertaining. Since this your honeymoon, I would try the restaurant right on the water in Vernazza. Request a table outside closest to the sea. You will need a reservation which should not be a problem since you are staying three nights. Make a reservation when you get to town. It is a bit of a splurge, but the food is great and the views are amazing. Check the RS Italy book for the name.
If you are really into hiking send me a message and I can give you some info on some hikes.

Sounds like a great trip and your time has been planned well for seeing these locations in the time you have overall.
Only thing not to discourage but just to dampen any expectations, your Tuscany countryside viewing will be limited to the views from Siena looking outward, you really don't have the time for a true drive out to the classic vistas you may be envisioning.
Would be amazing to stay for the Palio if you can work that in but those 2 days prior should be a very exciting time as well

Being your honeymoon I would keep any planning on the light and relaxed side, you don't have much time in each place and there is more than enough in each place to keep you busy. You will probably have your most down time in Vernazza depending on how much hiking you plan on doing but a lazy beach day is a good way to solve that.

Thank you all for the feedback. We are going to do our best with the limited time to tick off our boxes, but not going to rush through anything. I do have a few more specific questions though.
What is the overall experience for a side trip to Murano and Bursno from Venice. With 3 nights in Venice, is it worth our time to head there? Or is there something else in Venice we should focus our attention on?
Our time in Siena is most limited and during a unique period. Any other general advice for handling the lead up the the Palio? Or any other restaurant/places to see/things to do advice?

One question we do have is for train travel between destinations. From what I've read it seems that we should be able to book tickets once in Italy to get around either at the station or using trenitalia. Do I have the right idea here or off the mark?

Thank you again for your help.