March or April Trip

I'd go with Itinerary 1, but see if you can just fly open jaw into Amsterdam and home from Munich.

When to go is easy, as late in april as you can, unless you like cold and rain. It may still be cool and rainy in april ( my daughter flew into gemany this past april to start a 11 week long trip) but it will be better than march.

Oh yes, i like first itinerary way better and i too would look at open jaw flight, into amsterdam and out of munich.

Where you flying from?

I would definitely choose Prague over Frankfurt. And I'd spend more time in Berlin and less in Munich, but since your girlfriend has been there . . . .

April is better than March because the days are longer, more so because you'll be on DST. Take the Easter holiday into account and plan your trip around that. Decide where you want to be on the holiday and remember that public transportation around then may be very crowded and/or curtailed. That's school/university vacation, so there'll be more students traveling then, maybe you'll need to book hostel rooms in advance. Or you may want to start your trip in March and avoid the holiday period.

I too second Chani's thoughts. Berlin needs at least one extra day.

Easter falls mid April, so places will be busier when the schools and universities are on holiday - usually for 2 or 3 weeks.

As flights have been available for months, if you are travelling at Easter, look to book any flights within Europe asap, as prices only head one way. Skyscanner maybe useful or check out the airlines themselves such as Easyjet. For rail travel, look at seat61.com.

The clocks change at the end of March, so it will get darker later if you travel in April.

I would scratch Frankfurt from your choices. There are things to see in the area, but Frankfurt doesn't compare to the other places you mentioned as what you didn't mention.

Why choose cities so far apart as Amsterdam and Berlin or Prague? Why not fly into Munich or Berlin instead of Amsterdam and concentrate in Germany, Austria and Czech Rep.?

There is a lot to see in Netherlands, Belgium and Luxembourg, if you choose to stay in that area.

If you go to Germany, I recommend you consider taking The Romantic Road that includes some beautiful medieval cities like Rothenburg on the Tauber, Dinkelsbuhel and Donauworth, as well as Augsburg, Oberamergau and Garmisch.

Thanks for all the responses! Very insightful. To answer some of your questions:

We will be flying out of St. Louis,Mo. We were looking at a little extra time in Munich because we may do a day trip down to Salzburg. Also Amsterdam is just somewhere that we put as a must when we were decidedingb the trip and it's a little cheaper for us to fly into.

Schiphol is my favorite airport, I try to connect through it when possible, or spend a couple of nights in Amsterdam.

I would try for as late in April as possible, for the weather and the slightly longer days.

That is all the more reason to fly into Amsterdam and out of Munich. I don't see any significant price difference vs round trip to Amsterdam and both have single stop options. That will save a whole day over returning to Amsterdam the day before in order to get a flight back to STL.
Prices looks like they start rising if the trip starts after about April 6.

I'm using google flights to watch multiple fares. Hoping for them to drop under $1000 if possible. But I don't know if I will be able to get an open jaw under $1,000. However open jaw does save us the fare back to Amsterdam.

Usually open jaw costs about the same as, or a little more than, round trip. But it saves you the time and cost of backtracking to Amsterdam, giving you more time in Munich or wherever. I agree with others that Frankfurt doesn't have that much to offer, Prague would be a better choice.

The reason we were looking at Frankfurt was because my Aunt had live in weisenban for 5 years and had recommended it. However Prague has a big draw as does Salzburg. We are leaning towards the possibility of an open jaw flight and seeing Prague for sure.