Southern Germany itinerary help

First of all, why don't your fly United Express into O'Hare and catch a non-stop connecting flight into Munich?
Since you'll already be in Munich, why don't you spend all your time there on front end touring the city? It takes a good day to get your internal clock turned around. Then rent a car and hit the road.
The train service between Munich and Prague is not great @ 7 hrs., and often people take a 5+ hr. bus. It's much more preferred to take a 1 hour flight between those cities. Also, Prague is not a good city to fly back to the U.S. from as you'll have to fly to another European gateway city to fly back to the Midwest. (Only Delta has flights to North America and they're seasonal.)
Have you considered axing the Prague leg, and flying into Budapest--another great city that's easier to get to? The cities are somewhat alike, but the atmosphere in Budapest is better and it's much cheaper to travel there.
We've taken a counter clockwise trip a couple of times out of Munich going to Fuessen/Neuschwanstein, down to Innsbruck, around to Salzburg/Berchtesgarden and back into Munich. From there, you could catch a plane/train to other cities. You just have so many options that may be better than the schedule prepared by the travel agent.

What do you mean spend all the time on the front end of the trip in Munich? Like, not goto Berchtesgaden/RobT/GP? Those are must see places. We'd rather spend more time in the smaller towns, though we are interested in Munich. I'm no good at looking for flights and things (hence the travel agent). I've never done any international travel. Do her flight plans not look good? She had originally had us flying from Munich to Prague but changed it to the train, but a plane would be faster. Also Prague is a must, we have a friend there we want to see.

I think David means ( and I agree):
Fly into Munich, 3 night
Arrival day. _ get oriented and relax.Sight see the next 2 days
I would suggest the train or bus to Rothenburg ob der Tauber, 1 night
-Nightwatchmen’s Tour, Medieval Crime & Punishment Museum
Return to Munich and get car or get car in Rothenburg ob der Tauber
Then head to the
Drive to Garmisch-Partenkirchen, 2 nights
-Hike Partnachklamm or Hell’s Gorge, Zugspitze
-Neuschwanstein, Hohenschwangau
-Oberammergau?
Drive to Berchtesgaden, 1 night
-Eagle’s Nest, Berchtesgaden National Park
-Chiemsee vs Konigsee?
Drive back to Munich, return car,
Train or flight to Prague, 4 nights
-Kutna Hora
-Pilsen
-Loket castle?
-Rabi castle
Fly home from Prague
Flight: Prague -> New York -> Minneapolis -> Fargo

You will be exhausted after a wedding and a long flight. I think it is a good idea to start your trip with a couple of nights in one place.
I enjoy train travel and use it as a time to regroup . We did fly from Munich to Berlin- found that the time needed to get to airport/thru security and then from airport to Berlin hotel was more stressful and did not compensate for the shorter flight.

I see, yeah I feel like that makes more sense to spend more time in Munich at the beginning and just use public transport to get to RodT. It sucks we still have to go back to Munich to return the car/get plane to Prague or take the train to Prague. I was also thinking we could not take in the Schlosshotel Harburg and instead tack that night onto the Bercthesgaden stay.

Maybe we could drop our rental car off in Salzburg after Berchtesgaden then fly from there to Prague?

You definitely don't want to drop the car in Salzburg unless you want to incur a large drop off fee for returning it in another country. You have way too many things on your list of things you want to do than you have time to do them. It takes time to change locations. Spending one night somewhere gives you a partial day there. You may have to scale back on your must sees. I would pick up your car in Munich as you're leaving and drive to Rothenburg. From there drive to G-P. With 2 nights you will only have one day. You will probably need to choose between hiking and castles. Castles need an advance reservations. Be realistic about your time.

Wouldn't it be a lot better to start with the trip to the south of Munich, return and take the train to Rothenburg. Then instead of returning to Munich, take the train (and bus) to Plzen before continuing to Prague. That should cut down on your travel time a bit.

Where would we fly into if not Munich, though?

For me the itinerary seems pretty busy. I think you need to narrow on what you really want to see/visit. Oberammergau might be overkill after the older areas/highlights of Garmisch and Partenkirchen. I would skip Chiemsee and the Eagle’s Nest and go with Königssee (Berchtesgaden National Park) and take a day trip to Salzburg (make time for it). Your practically there in Berchtesgaden. Adjust for the weather. The Fischunkelalm on the Obersee (Königssee hike) may not be open in early May. Pilsen is OK, but not sure it's worth the time and watch your wallet there.

I'm definitely thinking Konigsee instead of chiemsee. The eagles nest I think we would like to see, my dad has early memories of going there when he lived in Germany as a kid and I'd like to go there as well. I'm not very interested in Salzburg. Pilsen is also a must, it's where my husband's favorite beer is brewed. I know the itinerary is packed, I figure we can fly by the seat if our pants a little and skip things if we are tired or weather isn't good. I'd rather plan for more and skip things on the fly than not plan enough if that makes sense.

Unless you really want to see the Schloss Herrenchiemsee on the Chiemsee Herreninsel, the Königssee in the Nationalpark Berchtesgaden is hard to beat for beauty. It's been some time, but you could safely park at the Pilsner Urquell Brauerei and walk into the old city central of Pilsen. I'd still keep Salzburg as an option as it's a 30-45 minute drive from Berchtesgaden. you can drive secondary roads to avoid the toll sticker requirement for the Austrian Autobahns. May can be fickle weather-wise. Been to Königssee in early May on a beautiful bluesky day, and Salzburg the next day in pouring rain.

I don't think we'll have a car in the Czech Republic, so we will be using public transport so parking won't be an issue. I am worried about weather, we chose May (mid to late) because of budget, things start to get much more expensive in summer proper :(

Just be flexible, have good shoes, a rain jacket and an umbrella handy. A small backpack comes in handy to carry them (where allowed).

Where would we fly into if not Munich, though?

Munich is a big hub, so it is probably a good idea to fly there.

Maybe we could drop our rental car off in Salzburg after Berchtesgaden
then fly from there to Prague?

Unfortunately, there are no non-stop flights to Prague from Salzburg (https://www.salzburg-airport.com/fileadmin/user_upload/pdf/Flugplan_Sommer_2020.pdf), so you would have to connect somewhere, defeating the time benefit of flying.

Also... picking up a car in one country and dropping it in another country generally generates a BIG service charge.

On Eagle's Nest (German = Kehlsteinhaus)... it opens sometime early to mid May (no exact date). A bus takes you from the Kehlsteinhaus Ticket Office/Gift Shop/Bus Stop near the public parking lot up the mountain to a bus stop at a tunnel that leads to an elevator that takes you up to the Kehlsteinhaus. The site does not open for the season until the road up the mountain is passable for the buses. With climate change, this tends to be early May, but it could be a bit later.

If you're going to fly into Munich, I agree that you'd be better off spending some time there while you reset your internal clock. But there's really not much difference between Munich and Garmisch; it's only an hour and a half south. Go that way first. Partnachklamm and the Zugspitz (provided the weather is clear) are better than anything Oberamergau can offer. Plus, this is a Passion Play year, so Oberamergau is best avoided unless you're doing that.

You just can't do Berchtesgaden, and Cheimsee in a day. A day each, yes. Even then you'll be rushing things.

It's probably actually faster to take a train to Salzburg and from there to Prague than to do the Munich-Prague direct. If that's true, I'd seriously consider doing that instead of Eagles Nest, etc.

As noted you can't see Prague and all the sights you've listed in four days. Not unless you just want to run from one place to another. I think you could easy do Prague in a couple days, then train to Pilsen for a day, then to Nuremberg, then Rothenberg odT, and fly home out of Nuremberg. If you can't get a flight out of Nuremberg you're just a couple hours (or less) by train from Munich or Frankfurt, and there's going to be a flight from one of those.

To me it makes a lot more sense to do a loop (and I've done that loop before, it both directions). Plus, if you do that route you can easily do it without renting a vehicle. If you do rent, you'll be returning it in the same country.

So... you could drop your rental car at Freilassing, about 30-40 minutes from Berchtesgaden, catch a 10-minute train to Salzburg Hbf, and then head to Vienna and on to Prague.