Prague is probably my favorite place in Europe. It's what I thought Europe was in my mind. The old town castle quarter areas are so cool. Very cheap Pilsners all over too. Budapest reminded me of Prague in how it was split by the river. Found it to be very inexpensive too. I liked the palace in Vienna but it felt a bit too fancy overall as a city. Have heard Salzburg and Innsbrook are outstanding from a scenery point. If you have been to Munich a few times maybe look for something like a tour of the 72 Olympic village type deal. No clue if that even exists. Dachau is also worth a stop of you haven't. I did Egypt in 2017 as an add on because I could fly back 1st/business from Cairo to the states. Found a 3 day guided tour of the pyramids, museums, churches, markets etc. Just be careful being there on a Friday. Getting to Alexandria or Luxor would be worth your time. In Cairo we did stay at a pretty nice place right on the Nile. Link
https://all.accor.com/hotel/5307/index.en.shtml
They were able to arrange a handler of sorts that got us through Customs then to and from the airport. Saved a potential headache
As far as the long travel times if you can use airline miles do it. Or at least book an exit row on the long legs. I am flying from Omaha to Ho Chi Minh for 70k miles and that gives me first/ business the whole way. That bed isn't quite long enough for me but I'm not gonna complain about my bed on a 12 hour flight. Lounge access is another perk. Don't knock am airport shower until you have tried it. Unbelievably refreshing