Two days in Bavaria - Help needed in Itinerary

for Option 1 - are you sure you can do all that in one day?

for Option 2 - why go to Munich if you spend no time there? Don't underestimate the transportation time it would take to either of those places on day trips from Munich. Most of your days will be riding trains/buses.

I completely agree with Stan. Why go to Munich if you spend no time there? There are plenty of things to see in Munich without going on side trips. Stay there or change your itinerary to spend more time in Munich including the side trips.

Where are you going next?

Munich is our last stop. Tickets are booked, can't extend.

Our trip high level itinerary.

Rome 4 days (include one day trip to Florence)

Amalfi coast 4 days (base in Salerno)

Salzburg 4 days (side trip to berchtesgaden and Zell am see)

Munich 2 days.

Coming and going from Munich seems a waste of time and energy.

You could do 2-3 nights in Salzburg and 3 in Garmisch. Visit N'stein (if you must) from a Garmisch base; Mittenwald is very close for a half-day outing if you like:

http://hastingshouse.typepad.com/hastings_house_us/travel_in_europe/
http://www.karwendelbahn.de/page/en/startseite

Your tickets to Munich are booked - but you haven't booked to N'stein or to Garmisch yet, right? To Garmisch (or from Garmisch to Munich) you buy the Regio-ticket Werdenfels (€26/2, current price) at Munich station. The ticket is valid to Mittenwald on the same day:
https://www.viajarsiningles.com/wp-content/uploads/2016/12/mapa-trenes-ticket-regional-Werdenfels.jpg
https://www.gapa.de/gapa/GaPa_img-pdf/00_pdf/flyer_werdenfelsticket_deutsch-englisch.pdf

You may wish to drop either the Berchtesgaden or the Zell am See outing from Salzburg depending on the time required for your sightseeing goals in Salzburg.

Russ - what I meant was my fly out ticket from Munich is booked. If it is required to make itinerary change I can still do it and only on the day of flying I can go to Munich and catch international flight from there.

Of your two options, Option 1 is the most logical but that second day will be very full even if you have your own car but still possible to do. Here is a similar route that I recommended to a previous poster:

When we lived in Munich I took several guests to Neuschwanstein and here is the combination that seemed to work best:

Rent a car for the trip that morning and return it that evening. This goes against most logic for Munich and Bavaria but I found it was the best way to get the most out of the day as you can hit several spots on the way there or back to get more out of your trip. These extra side trip are not as easily done with public transport or a tour bus.

Start early in the morning, pack a picnic lunch, and drive via your favorite Alpine route (I liked going via Kochelsee, Walchensee, Garmish-Partenkirchen) to Schloss Linderhof for a brunch break. Continue on which ever route you choose to Füssen arriving noonish-2pm, picnic lunch and tour the castles. Done with tour by 4pm and head back to Munich via Wieskirche for another brotzeit snack break.

Yes this is a long day but after a lot of trial and error with taking family members and friends to Füssen this seemed to be the most popular. Just going to the castles and back left a lot of people feeling a little disappointed.

If the weather is poor this won't be a very scenic trip though.

DJ