Flying into Milan and out of Berlin...

For what to see in Switzerland, look at the Rick Steves book. He is not alone in feeling that Zurich is NOT one of the country's highlights. Although some do like it, the real glory of the country is the Alps. Unfortunately, you're going during a bad time for them (between winter skiing and summer hiking seasons, when it's often muddy). Luzern is not weather dependent, and is a nice town.

I'm glad you're seeing some sights in Milan; I happen to like it, although it's not the "Italy" that most American visitors seem to seek. If you're going to Lake Como, try to spend at least two days there. Rick is right that the purpose of going is "to see how low you can get your pulse" and "if relaxation's not on your agenda, the Lakes shouldn't be either."

Between Munich and Berlin, there are the large cities of Leipzig and Dresden (both worth a visit), as well as various small towns others will know more about.

I haven't been to Dachau (the concentration camp near Munich), but there's also Sachsenhausen, near Berlin.

Train will work fine for you. To find schedules, use the Bahn website http://reiseauskunft.bahn.de/bin/query.exe/en, following Rick's tutorial: http://www.ricksteves.com/travel-tips/transportation/trains/online-schedules. This will only have prices and allow purchase for tickets that start or end in Germany (so you can use it for tickets from Switzerland to Milan).

To find the least expensive tickets, here's The Man In Seat 61's list of where to buy them: http://tinyurl.com/bo8x6o6. You would still use Trenitalia for tickets within Italy.

Lisa,

I don't have any comments regarding AirBNB of Couch Surfing, as I would never use either of those. I have stayed in Hostels though and they provide basic, low cost accommodations. You might have a look at the HI Hostels website as they will likely have properties in all the places you'll be visiting. Having an HI membership will provide lower rates and preferred booking (over non-members).

Regarding the places you want to visit......

• Milan - I'm not a big fan, but if you haven't been yet I suppose it's worth a day or so. I was back there last September, and the area around the Duomo seemed to be much more crowded than I remember from past trips.
• Lake Como - were you planning to stay in Varenna (the usual favourite of many here)? That's an easy one hour trip from Milano Centrale. Don't bother buying tickets in advance as that's a Regionale train, so difficult to buy online and no price difference. Just buy at the station (I normally use a Kiosk) but BE SURE to validate prior to boarding the train on the day of travel, or you may face hefty fines which will be collected on the spot!
• Switzerland - rather than stay in Zürich, I'd suggest either Lucerne or the Berner Oberland. Which to choose will depend on whether you're more interested in a historic city or alpine scenery.
• Munich - for the trip from Switzerland to Munich, you may be able to save money with a pre-purchased ticket. I haven't checked so will leave that to one of the Germany/Switzerland rail experts here. Check the bahn.de website for details. Visiting Dachau is very easy. You can either go on your own or go with Radius Tours. I realize you don't like tours, but wanted to at least mention it.
• Salzburg - that's a reasonable option for a day trip.
• Berlin - * for the trip from Munich to Berlin, a pre-purchased ticket may be a good idea. There's LOTS to see in Berlin, so I'd allow at least four days, which means you may not have time for any intermediate stops between Munich and Berlin. As a previous reply mentioned, you could also visit Sachsenhausen from Berlin, either on your own or with *Original Berlin Walks. As I recall, the trip is about an hour by train to Oranienburg and then there's a short (~15-20 minute) walk to the camp. I again suggested a tour as I find that I learn a lot more about the history, and the guide on the tour I took was excellent.

Regarding rail trips, you'll have to look at each segment you'll be travelling in order to determine whether a pre-purchased ticket will be a good option. If you're using the "faster" trains such as the Freccia high speed in Italy, those typically have compulsory reservations which are specific to train, date and departure time so you'd have to be willing to commit to a particular train. The cheapest Super Economy tickets are non-refundable and non-changeable, so choose carefully! If you're using Regionale trains, the easiest way is just to buy at the station when you arrive there (I usually buy tickets the day prior to travel and then just validate before boarding).

Buying all your train tickets in advance is not a very convenient option for every leg of the trip, but you could do that for a longer, more expensive leg, such as Munich-Berlin, sold with advance discounts on the same web site that we use for most train schedules. Tickets from Milan to Lake Como and the border are cheap to buy there in the stations. Since your trip is focused on Switzerland, a Swiss Travel Pass can be a good value to cover all kinds of transportation and also museums, offered in choices of 3, 4, 8, or 15 consecutive days, or the same choices for "flexi" days spread over a one-month window.