I would cut Croatia and Cinque Terre; too out of the way for a trip like this even though it sounds exciting!

Switzerland is a beast of a place to plan, especially for only 1-2 days. Not to mention Switzerland's an extremely expensive country, for real! As Rick Steves says, assume you will return!

I would switch some of the cities around to look like this:

London - 4 nights
Paris - 5 nights (fly)
Rome - 5 nights
Florence - 3 nights
Venice - 2 nights
Salzburg/Hallstatt - 2 nights
Munich - 3 nights
Prague - 3 nights
fly home

This is a personal preference, but I would want to hit up the massive cultural cities in the beginning when you have the energy. I once did Venice>Florence>Rome and wish I had done the reverse because Rome is another beast of a city that requires a lot of planning and patience if you want to see all the cultural sites.

" I'm really torn between seeing the "highlights" as it's my first time and trying to take a more Rick-Steves-esque Backdoor trip and go to more out of the way places."

I'd be inclined to the latter, or at least a mix. So while I see what everyone is saying about adding more time to Rome, Paris, and London (these cities do take more time to do justice), I would actually cut a big city or two in favor of smaller places. It will add variety to your trip, change up the pace, and give you something to see beyond capital cities and tourist scrums.

Also, be realistic in how much time and energy you'll have day trips. By the time you get to Rome you may not care to see another single ruin and may have no desire to hop on the train. If you are planning these longer day trips, allot more time in your base city.

oedipamas makes a good point: when we went to Central Europe, we had planned to visit Berlin, but after seeing Venice, Vienna and Prague (and planning to visit Munich before flying out) we were "citied out" and decided to see more of the country. We took a fairly leisurely drive back along the Danube to Salzburg and Hallstatt. Glad we did it, although we still need to see Berlin, etc.

Wherever you hit first - probably London . . . You need to build in at least one extra day for logistics and mainly getting over the jet lag. So if you think you can see the highlights of London in 4 nights/3 days (you can't really but never mind) Then you'll need a minimum of 5 nights/4 days to net you 3 full/usable days.

There are overnight trains between Munich and Prague and if going in the daytime I believe the bus is quicker than the train.

In general, there's no point in taking a fairly long trip to spend one night in a place. You have no useful time that day to see anything, and the next day, you have to pack up and leave the hotel fairly early. Most hotels will hold your bags until you come back for them a few hours later, but picking up the bags also takes time, and if you have a fairly long trip that day as well, you really have no time to see anything.

Figure out what time you'd arrive in these places, and what time you'd have to leave the next morning. Add an hour at each end, more if it's in a city and you won't be staying near the train station. Also allow half an hour or more for picking up luggage. You'll see that a lot of your one-night stays are pointless.

can't speak for other places, but for Dubrovnik you don't need to spend more than a day there (2 nights, one day).
Be prepared to be royally screwed by merchants in Dubrovnik for whatever you buy or book - they expect to earn a whole year of salary in two-three months of tourist season.
Zagreb, otoh, is very nice, and I would plan on spending 3 days there (4 nights) - simply walking around. it is a very nice town.
If you have a day to spare while in zagreb, drive or take the bus to Plitvice via Karlovac and Slunj. Don't take the motorway, go down highway D1 which goes through Slunj.
Make a pit stop in Rastoke; a samll place techically part of Slunj.