Purchasing Rail Passes in Switzerland and Italy - through Rick Steves?

Don't get a pass for Italy, its a waste. With only a very short train ride from the Italian border to Lake Como (where? its a big lake), followed by a train to Parma, which can be done with cheap regional trains. It is not worth considering.
There are many options for Switzerland. The Half fare card for 120 chf may be your best option.
http://www.sbb.ch/en/leisure-holidays/holidays--short-breaks-in-switzerland/swisstravelsystem.html

The only sale currently is a $50 coupon code to use on first-class passes purchased through the link below. We recommend the cheaper second-class passes, instead. Other sales offers are certainly possible before your trip; you'll just have to keep an eye out. (US prices are also subject to change based on Swiss/US exchange rates. Passes are also sold in Swiss stations.) Our recommendation is usually to choose the Swiss Travel Pass the best fits your number of train travel days. You could do more math and still come out with more than one option costing about the same.

You could use a Flex version of the pass for 3 days of travel in a month, with Half-Fare Card Combo, at an up-front price of $313 per person. Use those 3 days for as much travel as will fit until midnight (trains, boats, buses, city trams, museums). In between those three days, during your stay in Muerren, you can show the pass and get 50% off any transportation, except only 25% off the leg from Wengen to Jungfraujoch. All of these discounts will add up; see the regular prices listed at http://www.jungfrau.ch/en/tourism/travel-information/tickets-rates/muerren/fares-for-individual-travellers/.

Your travel time does not fit within a 4-day consecutive pass ($263 per person) but you could choose that with the plan to use it Sept. 30 - Oct. 3. That would give you fuller coverage on lower-level transport (below Muerren and Wengen), but would not cover train or any sightseeing on your arrival day in Luzern, for instance.

You can buy Italian train tickets at a station in Switzerland and/or Italy, no deadline to do so, and that's the easiest plan for unreserved regional trains. To reserve ahead with advance-purchase discount on faster Italian trains, such as your Milan-Parma leg, you can add that ticket in the same shopping cart when you buy the Swiss pass or you can book it separately now at www.trenitalia.com.

For the most comprehensive train schedules and route options to Lake Como, use the Swiss site, www.sbb.ch. You didn't mention which town on Lake Como and which route you want to take there. For instance, if you want to travel the slower "Bernina Express" route via St. Moritz to Tirano, then continue south along the east side of Lake Como to Varenna, this site will reflect those schedules, whiles some others do not.

Thank you both for your replies.

I believe we will purchase the 3 day Flex Pass with the Half Fare Card based on your feedback. Thank you - this information does help me alot! We will be staying in Varenna (Hotel du Lac per RS's suggestion) and will probably go the direct route to Lake Como from Murren. I understand that we can purchase our tickets at the station once we reach the border (would that be Chisso?). I will take your suggestion also to reserve ahead with advance-purchase discount on the Milan-Parma leg. Do we order both through the RS website?

Another question - does the lifts to Schithorn and Junfrau count as a "travel" day?

If you are getting the Half Fare Card add-on to the Flexi Pass, use the Half Fare Card for those trips assuming you are not doing any other trips that require you to a flex day. It will be the same price for the Schilthornbahn, and if you use a flex day you will pay exactly the same price (50% off). The Jungfraujochbahn only gives 25% with the Swiss Pass flex day above Kleine Scheidegg, but if you use the Half Fare Card you get 50% off of the entire journey which works out to less in total.

As far as going from Milan to Parma, you can take an all 2nd class Regionale train for 10.90 euro, no reservations required or available, at 12:15 that takes 1 hour and 25 minutes. There is also a Regionale Veloce at 13:20 that take 1 hour and 34 minutes, but also has 1st class for 17 euro. You don't need to buy these in advance. However, there are no ticket facilities at Varenna station, so you need to buy at a travel agency in town. Buy the Milan-Parma leg at the same time. You just need to remember to validate the tickets at the stations. Rick Steves doesn't sell these tickets, you have to get them yourself.

There are lots of ways to get from Muerren to Varenna, none of them all that direct.
1) Muerren to Milan via Domodossolo, then backtrack by train north to Varenna
2) Muerren to Como via Luzern, then bus or taxi to the ferry dock, then ferry to Varenna.
3) Muerren to Lugano via Luzern, then bus to Menaggio, then ferry to Varenna.
4) Muerren to Tirano via Luzern and Chur, then train to Varenna
5) And yes there are even more complicated ways.

cstretco to clarify, the trip to Jungfraujoch is not on a lift, it is on a train. Expensive, and much of it in the dark as you are going through a tunnel up the mountain. Takes about 1& 1 /2 hours to get up there, so uses up a good part of a day to get up & down.

Thank you so much for all of this information. It is very helpful.