Train Planning HELP

In Italy all trains except Regionale require a seat reservation. Approx 10 Euro per seat/ per leg. If you willing to lock into an advance schedule, the deep discounts available for on-line purchases easily beats a rail pass in Italy. Most rail systems in Europe have moved to discounting advance purchase ticket on line. But those tickets are fixed, and often no refund or exchange if you miss the train or want to change.

Where are you planning to fly to coming to Europe? There is no airport in Cinque Terre. Closest is Pisa, and there are a few flights to Pisa from North America in the warmer months. Milan has lots of flights, as does Rome, but if you start in Venice, you cut out one train leg. So into Venice and home from Munich makes the most sense.

Sam, we're actually flying in to Munich and going straight to Bulgaria to visit my sisters birthplace. From there we're turning this in to another trip, flying direct to Pisa and training to CT. We'll then be flying home from Munich, that's why we were ending in Munich

Do you have your flights booked yet and what time of year? I see Alitalia has nonstop flights from Sofia to Rome in the $95US range. It might be easier to start there and take the train to CT from there.

Yes, we booked flights to Pisa for 23euros each:) Really I'm just needing help on the remainder of the trip

Instead of a Select pass for 2, 3, or 4 countries (you're barely traveling in Germany), I'd look at just a Swiss Travel Pass to cover most transportation within the Swiss borders and discounts of 25 or 50% on the higher mountain rides near Muerren. If your time there fits into 3 or 4 consecutive days, then that version of the pass is a handy fit. If you buy the pass ahead, then you can buy your Italian train ticket just to the border point, such as Tirano if you're heading straight north from Varenna, or Chiasso if you'll take the faster central line.

OK, Pisa to CT is a cheap Regionale train, no reason to use an expensive pass day for that.
Speaking of expense, I see a 4 country pass for 5 days of travel is $1644 for 4 people traveling together. Add in $90 of reservation fees in Italy, and you are paying $86 per person per travel day. Even if you just bought walk-up fares, you could probably beat that. Maybe not 1st class, but plenty good. Now if you buy nonrefundable advance purchase tickets, you could cut that in half.

So if I'm going to buy tickets in advance, is the best option to do that through the site for each country's rail system? I know that I've seen Bahn.com for looking up schedules but didn't see that you could buy through that. Thanks

Did you consider this routing ?
Cinque Terre>Venice>Innsbruck>MurrenSwitz>Lake Como
Fly Milan>Munich

OK, here goes.
1. Pisa airport to (since you did not say where in the Cinque Terre you were staying) Vernazza. 12.60 EUR including the shuttle bus to Pisa Centrale. Buy when you arrive. Could be a bit more if an IC train is used between Pisa and La Spezia.
2. Vernazza to Venezia S. Lucia. 42.40 EUR. Will vary by your travel date. Buy at www.trenitalia.com.
3. Venezia S. Lucia to (since you did not say where on Lake Como you were staying) Varenna-Esino. 36.60 EUR. Buy at www.trenitalia.com.
4. Varenna-Esino to Milano Centrale. 6.70 EUR. Buy at the travel agency in Varenna.
5. Milano Centrale to Muerren. 104 CHF. Buy at www.sbb.ch/en.
6. Muerren to Innsbruck. 64 CHF. Buy at www.sbb.ch/en
7. Innsbruck to Munich. 19 EUR. buy at www.bahn.com

Now that comes to about $305 per person assuming 4 adults. Children will be less. You didn't say.
If you will be taking lift excursions like the Schilthornbahn in Muerren, a Half Fare Card might be in order. It is 120 CHF per adult. That would cut the the Milan-Muerren price to 67 CHF (reduction is only for the portion in Switzerland. Does not do anything for the Muerren-Innsbruck leg, since it is already a discounted fare.

geez Sam has it covered, hey Sam can you do my income taxes next year, hehe...Anna I would add that when you arrive at Pisa know that you can purchase the shuttle ticket from the bus driver, you dont have to stand in line at the trenitalia window for a ticket. When we arrived the line was quite long at the ticket window in the airport. You can get euro's at the ATM in the airport and then pay cash to the shuttle bus driver for the ride to the Pisa station, he even had change for reasonable size bills.
When you transfer at La Spezia be sure to notice on your tix which bin (binara-train platforms for boarding) your train leaves on as at both Pisa and La Spezia there are several bins and you reach them from underneath. I'm not sure where you are from but this site was helpful to me as a train novice. http://www.seat61.com/Italy-trains.htm#.VR1X5st0wfg

Y'all are amazing, this is so helpful. We've decided we're going to do pre-purchase point to point tickets due to your help. I read on another post to not buy Regionale tickets ahead of time. Is there a reason I choose one type of train over others or do they just have different time options? If one doesn't seem very cheap, do I then bank on finding a cheaper Regionale ticket once there? Thanks again

Basically, the higher prices for intercity and freccia trains get you faster trips and somewhat more comfortable seats. I don't find the regionale seats uncomfortable, so I always look carefully at the trip duration to be sure the time difference is worth the extra charge. Sometimes it isn't; I'm not paying an extra $18 to save 15 or 20 minutes. If you're able to pre-purchase non-regionale train tickets and can snag the super-low-cost non-refundable tickets, I assume the prices will always be a good deal, considering the time saved.

The reason to choose one train over another is speed, frequency, and fewr changes on routes between major cities. For instance, (again I'll use Vernazza) to Venice is 4 to 5 separate trains, and 6 to 7 1/2 hours. Using a mix of Regionale, IC, and Freccia trains, it is 3 or 4 separate trains, and 5 to 6 1/2 hours. The Regionale prices are fixed at 31.50 to 32.50 EUR depending on the route, as low as 32.70 EUR when bought up to 4 months in advance, but as high as 87 EUR when bought day of travel.

Venice to Varenna-Esino is 3 Regionale trains, take a bit more than 6 hours and costs 24 EUR all the time. Using the Freccia it is 4 hours with one connecting Regionale from Milan to Varenna-Esino. It can be as low as 16.60 EUR 4 months in advance or as high as 45 EUR bought day of travel.

Going to Muerren is not as advantageous as Swiss trains are the same price all the time, you can take two Regionale's to Domodossolo for 15.20 EUR in 3 1/2 to 5 hours, then you will be on Swiss trains the rest of the way. It is 73.60 CHF the rest of the way to Muerren all the time.

Muerren to Innsbruck can be done inexpensively because SBB will sell you a saver fare ticket on the Austrian Railjet from Zurich to Innsbruck if you buy it well in advance.