Rudesheim is not in Bavaria so not part of the Bavarian Ticket, which can be bought in any train station I believe in Germany. You could also take the Romantic Road bus from Wurzburg to Rudesheim.

So many trains the rarely sell out and since seat reservations are not required you can usually get on a train even if all seats are full and at the next station when someone leaves sit down - or at the worst have to go first class where there are nearly always empty seats. I would not worry about that. You can easily make seat reservations as you go along at stations if you see things are mobbed more than you thought they would be.

"2. Cologne to Rudesheim: €38 (saver fare) - 1 change, EC, VIA"

That's a good fare. I take it you're on the EC to Koblenz and proceed from there on the VIA. Please note that while you must use the EC train scheduled for Cologne-Koblenz, you do NOT need to use the scheduled regional train for Koblenz-Rüdesheim - you can use ANY VIA train(s) that day on that route. If you want to stop over in Braubach for Marksburg or a look around (the TI office will hold bags) or have lunch in Koblenz or whatever, that's fine.

"3. Rudesheim to Rothenburg (3 hr 39 mins stopover at Würzburg to sightsee, arrive at Rothenburg at 4pm) - €48 (Question: Is the Bayern Ticket available for this route? Will save €20)"

No, no Bayern Ticket... I take it that to reach Rothenburg you are booking a VIA - ICE (Frankfurt-Würzburg) - RB - RB sequence of trains. Again you will have to ride the ICE train as scheduled but the others are flexible. If you are done earlier or later than your stopover stipulates, it doesn't matter - just take any RB trains at any time you like that day between Würzburg and Rothenburg.

The Bayern Ticket is sold on the spot with no possibility of reservations and no reference at all to available seating. It is theoretically possible that you might board a train and have to stand for a while.

The Bayern ticketn for Rothenburg-Munich and Munich-Salzburg means a slower trip than you'd have with a saver fare. You can check prices and travel times to see whether it's worth it or not. To find travel times on the regional trains only (which you use with the Bayern Ticket,) remember to specify "only local transport" under "means of transport" at the DB itinerary page

You do not HAVE to buy reservations for the saver fare journey either... the only seat reservations possible anyway for Rüdesheim-Rothenburg would be for the one Frankfurt-Würzburg ICE train (which is only about 1 hour of your roughly 4-hour journey.) You don't get reservations on the VIA or RB trains.

Note that instead of the Bayern Ticket (€28) you can use a "Guten Tag Ticket" (€25/2) on any of the M (Meridian) trains between Munich and Salzburg. Same rules of use apply.

Many thanks to PalenQ and especially appreciative to Fuss for providing such detailed and helpful comments. It is our first visit to Germany and am grateful for all the help rendered - which I am certain has made the logistical aspect of our trip much more manageable.

Will proceed to purchase the relevant train tickets, and will bear in mind the tips given above re train schedules.