You have a lot of questions in that post, and a lot of stops in your trip.

While it's tempting to do and see as much as you can, a bit of advice I would give is to plan at least some of the trip to be slower since it's your honeymoon. It may not apply to the two of you, but after all the stress and activity of a wedding, many people appreciate some down time to just relax with your new spouse. At least give that a thought. With 20 days, you still have plenty of time to see stuff if you relax for a couple days.

As for the UA miles, if you have any flexibility on your dates, you might be able to find Saver awards. But IMO, using ~200k miles for a great trip and honeymoon are worth it.

Transportation: I would probably stick with trains as much as possible between cities. They're easy and they generally run on time in this part of Europe. It takes away the stress of having to navigate unfamiliar territory and possibly reading signs in a language you don't speak. Once you finalize your itinerary, check individual tickets vs. the rail pass. I've never found a pass worth the money, but maybe it will be for you if you actually work in all the stops in your list. You'll want to rent a car for certain trips, such as Cinque Terre (in my opinion). But do this as necessary, not for the whole trip. 2 bags per person is fine on the train. I typically have a rollerboard and backpack. From airports, it may be easiest to take taxis to your hotel. It depends on where your're staying, and if it's easy to get to using other means.

My final suggestion is put together your itinerary of each stop and how many days you THINK you'll want in each location. Remember to factor in travel time (while it won't be perfect, you can simply Google something like "train time from Venice to Rome" and get a rough estimate). Post it back here. You're more likely to get helpful feedback if you start with something detailed rather than just asking an open-ended question of how many days to spend at each place.