Travel by Train/Rail through Germany

I would not bother with night trains, unless for nostalgic reasons because the last German one will be on December 8. They are being eliminated. The distances just aren't that great.
Frankfurt to Berlin and Berlin to Munich should be bought now on-line assuming you want to save money and you know about what time you want to travel, at www.bahn.com.
Munich to Fuessen (where Neuschwanstein is) and Salzburg can be done with Bayern tickets you buy out of vending machines at the train station. 28 EUR total covers two of you for all day after 9 am weekdays, all day weekends, regional trains only.

Hi Sam, thanks for replying. As of now, we don't know how long we plan to stay in each city. Is there another train option for spontaneous city hopping?
Is the day ticket not recommended for traveling throughout Germany?

If you don't know what the days are, look at what the prices are for Flexpreis tickets and compare that with what you would pay for a railpass. You can always buy tickets at the last minute at the station for the Flexpreis.
I would not go with regional trains for the big journeys as it will be slow with many changes. There will be frequent ICE direct trains on those routes.
Bayern tickets or other laender tickets are for regional trains with no reservations, so they are always "flexible".

I've provided my itinerary above

Well, not exactly.

Are you arriving in Frankfurt and spending a few days there, or going right to Berlin that day? If going right to Berlin, you should have bought your airline ticket through to Berlin. It will probably cost you more to go from Frankfurt to Berlin by train than it would have to go to Berlin by air as part of your ticket. If you are spending a few days in Frankfurt, using an advance purchase ticket to Berlin will save you a lot.

If you can commit to a specific train, you can probably still get a better fare from Berlin to Munich with a Savings Fare ticket.

The rest of the trip looks like a Bayern-Ticket will be the way to go.

If you cannot or do not wish to pin down specific trains and travel times to get those "saver fares," it will be expensive to purchase flex-preis tickets. FRA - Berlin costs E250/ 2 adults. Berlin - Munich is about the same. But you can get a 4-days-in-one-month German rail twin pass from DB for 2 persons at a cost of E308 total. Note that you can buy the pass in Germany at FRA airport if you wish.

https://www.bahn.com/i/view/USA/en/prices/germany/german-rail-pass-flexi.shtml

@ linlin....Keep in mind that while the night train in Germany, the CNL, will be discontinued there is still night service. That is done by the IC and ICE trains, which you still have the night train option available. It was almost like that this past summer taking the night trains in Germany if you did not want a sleeper or couchette which I didn't. That night service was carried by the IC and ICE trains.

thank you all so much for your responses. my current plan is to stay a few days in each city (i.e. arrive in Frankfurt, maybe stay 2 days; take the train from Frankfurt to Berlin, stay 2-3 days depending on if we need more time, then move onto Munich, etc).
However, it sounds like it would be much more cost effective to have schedule committed days in each city, thus I need to buy my Saving Fares tickets in advance.
I'm looking on bahn.com, I don't know which train station of each city to begin and end with (Frankfurt Main Hbf vs Sud, Berlin Hbf Sud vs Tief, etc).
Another question to throw out, how about flying from city to city?? Airfare appears cheaper and faster than train!

Frankfurt Hbf assuming you are saying in the center center city.
Berlin Hbf, but you may be staying else where. Berlin is a big city (Berlin ist so Gross, as Otto Reuter used to sing). So you might specify a destination closer to the hotel you are planning at staying. Maybe Berlin Savignyplatz, or Berlin Alexanderplatz. You can buy a ticket to close to your hotel if you know where it is.

@ linlin...Berlin Hbf (tief) means the lower level at Berlin Hbf , tracks 1 and 2.

Frankfurt Main Hbf is simply Frankfurt Hbf on the Main River. The Main River flows through Frankfurt. There are two cities named Frankfurt in Germany, the one in western Germany is called Frankfurt am Main, the other Frankfurt, a much smaller town, is on the Oder River, which is called Frankfurt an der Oder. You'll be using Frankfurt am Main Hbf. ...not Süd.

On Berlin: there is no Süd. There is the subway station called Südkreuz, (south crossing), some trains stop there. That does not apply to you. The other 2 stops are Westkreuz and Ostkreuz

You can get a day ticket in Germany for the whole country (known as a "Quer Durchs Land Ticket"). However, the Quer Durchs Land Ticket is not usually recommended for long journeys like Frankfurt-Berlin and Berlin-Munich because you are limited to local trains, which are slower and can have poor connection times.

Are you sure you don't want to commit yourself in advance to a travelling schedule? You have only two weeks for some four or five places you certainly want to visit. Your flexibility is limited, and you can be pretty sure you want to stay longer in Berlin than in Frankfurt, and that one full day is enough for Neuschwanstein.
The alternatives are not attractive. It's either stiff prices for a next-day flight or fast train, or a cheap but slow regional train for long distances (Frankfurt to Berlin on regional trains takes some eight hours!).

As Russ said, if you insist on full flexibility on the longer train routes, you'll do better with a German Rail pass. But I agree with tonfromleiden - you have less flexibility than you may think. Sure, you can add or subtract a day here and there, but is that worth the extra cost it will entail? Your call.

Hbf means hauptbahnhof, or main station.

"...my current plan is to stay a few days in each city (i.e. arrive in Frankfurt, maybe stay 2 days; take the train from Frankfurt to Berlin, stay 2-3 days depending on if we need more time, then move onto Munich, etc). "

So you'll travel maybe every 2 days - so maybe 7 travel days over the 15-16 days... and you want to spend more or less time here or there as you go...

Then you buy the German Rail Flexi twin pass for 7 days in one month for E408 for 2 adults. That offers full flexibility on any train at any hour of the day for a cost of E28 each per day.

You can price out the pre-purchased saver fare tickets if you wish, but I'm pretty sure they will cost more than that - and they will tie you to specific trains at specific times - and you will have to make all those decisions now for the best prices. No flexibility.

And if you decide later to travel on 8 days or 9 days, then you just buy a regional day pass for your shorter trips (like the Bavaria Ticket day pass.)

If you are just planning two major journeys, Frankfurt to Berlin and Berlin to Munich, just get the 3-day Flexpass. 287 EUR for a 2nd class twin. You can use the 3rd day for Munich to Salzburg and be able to ride an ICE or Railjet which are faster than the regional trains and you will not be restricted to leave after 9:00. You can return to Munich using a Bayern ticket.
Since 2 Flexpreis tickets for Frankfurt to Berlin is running around 260 EUR, you will just about pay for the pass in one shot. Berlin to Munich price is about the same. You may want to spring for reservations on those trips to insure you get a choice of seats together. It is only 4.50 EUR per person per reservation.

"If you are just planning two major journeys, Frankfurt to Berlin and Berlin to Munich, just get the 3-day Flexpass. 287 EUR for a 2nd class twin."

And do the additional travel days with the Bayern Ticket or similar regional day pass?

If this couple will travel by train 7+ days, I think the 7-day twin pass is likely the better choice. The thing is the excellent price - at €408.- the 7-day twin pass offers two adults 4 additional travel days for an additional €117 - that's €29 per additional rail pass day - the same price as the regional day passes for two adults. But unlike the day passes, the rail pass allows the use of ANY trains (IC, ICE, etc.) at ANY hour (no weekday 9 am restriction.) So with the pass linlin will have more flexibility and a larger radius of travel options - for no additional cost over the regional day passes.

Another question to throw out, how about flying from city to city??
Airfare appears cheaper and faster than train!

Don't look just at the flight cost and time. Look at the time and cost of the entire trip. It costs money to get from the train station to the airport; it also takes time (travel to the airport, check in, security, waiting to board, post-board/pre-flight time, flight time, deplaning time, finding ground transportation, travel time to downtown). Make sure, before committing to flying, that you know the cost and time to get to the airport from downtown and getting into town from the airport. The rule of thumb is that if the train takes 6 hours or less from city to city, you probably can't save time by flying.

"flying from city to city." Not an efficient option. You'll wind up wasting more time in terms of waiting.