Your first plan had 15 nights. The revision has 11 nights. What's going on there?? I actually think if you really want the cheapest airfare you should be flexible about the number of nights and dates - sometimes just a couple nights more (or less) from what you had in mind can be MUCH cheaper.
"You could spend the rest of your life in Europe and not see everything." True. It's also true that you could spend just a few days trying to see what the tourist brochures and some guidebooks tell you to see, and see very little of the country or its people. With that in mind, some comments about your plans for Germany/Austria...
Your plan to drop Füssen is probably a good one. Time consuming to get there and away, "fake" castles (19th-century residential palace made to look like a castle.) And it's pretty full of tourists as small towns go.
The other most touristy place in Germany is Rothenburg. So going out of your way to spend a night there is only wise if you just really want to be around international tourists and the waiters and shopkeepers that tend to your tourist needs.
Heidelberg is OK. It was mostly spared during WW II (unlike Rothenburg, which was nearly half destroyed, then rebuilt.) And it's a real (big) German town with a lot more than just tourist shops. But the "castle" in Heidelberg is, again, a palace rather than an authentic castle.
Munich can be good - depends on what you have in mind, I guess - there are many options there.
So here's a streamlined outline that I might suggest to my best friends...
Arrive FRA, catch a train only 25 minutes to the university town of Mainz (2 nights.) Settle in, see what you can or have the energy for that first day. Mainz is very walkable and has a huge zone for pedestrians only. Try the Königshof or the IBIS (closer to the old town) for a good price.
Day 2: See the Middle Rhine Valley by train and cruise boat. 40 authentic castles in 40 miles of river, including Rheinfels and Marksburg. Very cool old world towns like Bacharach and Braubach that are similar to Rothenburg but without the massive tourist horde.
Day 3: It's about 4.5-5 hours of train travel to Lucerne, CH. Stop over in Heidelberg for several hours (use station lockers) and enjoy the town. Then arrive in the evening in Lucerne.
The rest... Not sure how many days where. But with Como, Verona and Venice, it will be several. THEN... FLY back to Germany on a discount airline... to Munich if you like, then train to FRA at the end... or just FLY on a budget airline back to FRA if you decide to spend more time in Switzerland and Italy. Frankfurt itself would be OK to visit for several hours at the end of your trip.