Rail Pass Question: Germany, Switzerland, Austria

For Salzburg-Munich what you want to buy is a Bayern-Ticket from German Rail (not Austrian Rail) at the Salzburg station. You can use it after 09:00 on weekdays and anytime on weekends and it is only valid on regional trains, not express trains. It will cover your ride to Munich plus all your local transportation, including buses, in Munich all day long. It costs €20 if you buy it from a ticket machine and €22 if you go to a ticket window.

The first problem I see is Interlaken Ost (not Lauterbrunnen) to Salzburg takes at least 8 hours. I would not call that "afternoon travel".

Also FRA to Moselkern, time to hike to/from the castle, time at the castle, then travel to Baden-Baden would be a pretty long trip without jet lag. When is the plane scheduled into FRA?

It looks like you are underestimating travel times all over the place. You can get these times from the German Rail website. (It will work better if you spell Fussen as Fuessen).

I know that from Munich you can travel to Salzburg free with the city transport pass.

I didn't know that. If by "a free city transport pass" you mean that some hotels give you a Tageskarte for MVV, Salzburg is not in the MVV and a Salzburg hotel would not give you one, anyway.

You are trying to squeeze way too much into this itinerary and not leaving yourself time to just kick back and relax. For example Frankfurt to Burg Eltz to Baden-Baden? It will take 2 hours to get to Moselkern from Frankfurt, then a few hours more or less to see the castle (depending on whether you hike up to it or not), then 2 1/2 more hours to get to Baden-Baden, then 30 minutes to catch the bus into town. You need to rethink this one. I was just there and upon getting off the train in Moselkern I can tell you that there are no buses or cabs waiting around to take unprepared tourists up to Burg Eltz. Moselkern is not a staffed station. Unless you make arrangements you must follow the signs and hike up to it through the woods. By the way, what are you planning to do with your luggage while you tour the castle?

That said I recommend you investigate a German Railpass. They're available for a number of days (4, 5, 6, etc) depending on your needs and will beat the point-to-point costs for most trips. We just came back from a 2-week trip to Germany: 5 nights in Cochem on the Moselle, 3 nights in Baden-Baden, 3 nights in Rothenburg, and 3 nights in Munich. We bought a 6-day German Twin Railpass online from bahn.de (Rick Steves also sells it for a little more money on his website). The German Railpass is also good for travel to Salzburg and Basel, Switzerland.

Your first day sounds difficult to me, especially considering jet lag! Burg Eltz is about an hour hike both ways, and by the time you get out of the airport and to the town where the trail begins, the day will be wearing on. I'd suggest your first night in Cochem, which is a fairly short train ride to the town where you find the trail. BTW, the hotel just before you start up the actual trail makes a great picnic sandwich! You might consider sleeping in Gimmelwald or Murren instead of Lauterbrunnen - SUCH better views, you are up IN the mountains. I'd check out a rail pass for Germany/Switz. From a fellow Missourian!