5 day itinerary from Frankfurt to Munich

Cut the Black Forest and Baden-Baden, and I think you have enough time to adequately explore the Rhine and Mosel with a stopover in Rothenburg on the way to Munich. You could conceviebly see them on the way back to Frankfurt, but neither the Black Forest nor Baden-Baden are really that unique (and Rothenburg is not nearly as unique as advertised either, but it does make a convenient stop between the Rhine and Munich). If you really want to experience the ultimate German bathing experience, spend a day at Therme Erding near Munich. Baden-Baden struck me as the kind of place a Russian oligarc would bring his expensive 28 year old mistress.

As for "wine country", you didn't specify which one (Germany has several), but the Rhine and Mosel should fill that qualification. Pay particular attention to the stretch of Rhine between Wiesbaden and Rüdesheim on the right bank, I think some of the best German wines come from here, but it largely gets bypassed by foreign visitors on their way to the Romantic Middle Rhine.

3 days is not enough time for Vienna from Munich and then returning to Frankfurt, especially if you don't fly. Vienna needs several days, whereas the old preserved part of Salzburg only takes a few hours to explore- it's surprisingly small, about the size of a large shopping mall.

Thank you Tom for your reply. Would you suggest we use the train/public transportation or would renting a car be more beneficial for the first part of our trip?

I'll let others weigh in on that question. I've done it all by car, but then again, I lived nearby for several years and owned a car, so there was no reason for me to explore via public transportation.

I would, however, caution against driving immediately after a transatltantic flight. Give yourself at least one solid night of sleep first before attempting to drive.

Great advice Tom! Do have a favorite town to stay in the Mosel Valley? Any wineries that are must sees? Rhine cruise vs. Mosel cruise? I have read many opinions but it is nice to speak to someone who has lived there!

A one day river cruise (Rhine or Mosel?)
Burg Eltz castle
A visit to wine country

9/25: Train to Boppard for 3 nights. The 25th is the final day of the weekend wine fest - a very fun time.
9/26: Train to Bingen, stopping in Bacharach for 2-3 hours on the way; cruise to St. Goar (1.5 hours through the most scenic part.) Have an afternoon meal, visit Rheinfels castle right in town. Evening in Boppard.
9/27: Train to Moselkern for hike to Burg Eltz and back; train to Cochem for pm. Train back to Boppard.

Boppard is your best "old wine town" base for seeing both your Mosel destinations and your Rhine stuff. Lots of good lodging and dining choices compared with other Rhine towns. It splits the distance nicely for your day trips. Day outings by train are done easily and cheaply on local small-group day passes.

Boppard wine spot: http://www.deutschlandgourmet.info/bilder/gross/5710-Restaurant-Weinhaus-Heilig-Grab-Boppard.jpg
Old town in Boppard:
http://farm3.staticflickr.com/2769/4245012678_95c5c8b305_o.jpg
http://home.kpn.nl/JLKampen1961/alb/Rome/Pauze%20in%20Boppard.jpg
Gedeonseck near top of Boppard chairlift: http://ext.pimg.tw/samlucky5711/1379089584-1923285561.jpg?v=1379089585

Then if you're going to visit Vienna, spend 2 nights on the way in/near Rothenburg. Würzburg is a nice city nearby to stay in and/or visit. I find Rothenburg horribly touristy myself.

Thank you Russ and Lubitsch for your suggestions. I so appreciate your taking the time to help me.

I think we should skip Vienna and make that part of another trip in the future. Since you both thought we could do most of our travel by rail, is it best to buy a Rail Pass or get tickets as we go? I think I read that you need to get your passes before you leave the U.S. Is there anything else that I should get tickets for before I leave - castle tickets, Rhine river cruise tickets, etc? Or can we purchase those on the day we visit?

You can buy rail passes in advance from DB and from domestic agencies but you can buy them in Germany as well. That said a rail pass is overkill, IMO.

Train from FRA to Boppard for two will cost less than €40 for tickets bought at FRA airport's Regionalbahnhof station. You buy one-way tickets to Mainz (€4.85 each I think) and a Rheinland-Pfalz day pass for two for Mainz and onward (€29/2.)

The day trip from Boppard to Eltz and Cochem and back can be done on VRM mini-group ticket (€22.10/2.)

The cruise day outings I suggested would be easiest with the R-P ticket again (€29/2.)

The trip to Rothenburg on a pre-purchased Saver fare ticket is selling for €48/2 adults (using high-speed, long-distance trains where possible.) Buy it ASAP online for your travel date.

Once in Rothenburg or Würzburg, you're in Bavaria and can use the Bavaria ticket day pass (€31/2) as long as you stick to the regional trains. It's valid to Munich, Salzburg, and anywhere in Bavaria.

All the day passes and local tickets and the cruise tickets can be bought there. The Saver fare should be bought soon.

Thank you Russ....this is extremely helpful! Things are beginning to make sense:)!