Spend 1.5days at the Louvre in Paris, break it up into sections of history that you want to see. Gotta see all the Renaissance stuff on one day and then second half day see their Egypt collection from all the stuff plundered by Napoleon from Egypt.
Also see the Museum d'Orsay for all the impressionist stuff. Nortre Dame, Sainte Chapelle (especially the windows!!!). Have dinner in the latin quarter, be sure to have a kir royale as an apertif.
For food, French food is fantastic. Have lunch at a bistro, simple bread and cheese with a glass of the house red is wonderful. Stay away from anything that has the word RIS as part of the name. FYI ric is equal to rice, ris is not stuff you will want to eat. pan chocolate is joyful as a breakfast snack.
Do go tot Arc d'Triumph and go to the top, walk the Champs Elysee and window shop, if you have time a trip out to Versailles is something to do as well. Many, many things to do in Paris.
Munich is a wonderful city too. The airport is fantastic and offers easy train access to downtown. In addition to the castle that you want to see take a trip out to Dachau for a sobering reminder of modern man's cruelty to other human beings. In Munich the Marianplatz is something to beholds and of course you have to go to a beer garden in Munich!!! EAT!
Europe, where you are going is easy to survive on English, but learn a few local words and you will go far. Currency is all Euros and travel is easy on the train as well as intercity flights. Thankfully interEurope travel is not as ridiculous as American interstate flying. Power is all 220VAC 50Hz, check your chargers and see if they already support that voltage and then all you will need is a plug adapter. Europlug is what they use. If you have a GSM phone set it up for roaming but I highly recommend that if you contract is paid off on your phone to get it unlocked and then buy a local SIM card to save money. For example I am in Greece right now and am paying $2.29/minute with $.50/SMS outbound $.05/SMS inbound. France is cheaper at $1.29/minute.
Other than that what questions do you have?
Scott hit most of it.
I'd add Eiffel Tower (Tour Eiffel) and Sacre Cour to the list for Paris. You said you only have two days - given that, I'd not bother trying to vet to Versailles or Giverny, both of which should go on a future list.
Assuming you fly into CDG (I'll be doing ORY on my next trip), find the train station and get a 3 day transit pass that includes the RER & Metro. The RER runs from CDG into Paris & is better than a bus or taxi.
Dachau is a "must see", but is (truly) haunting. I like Munich - though there are some other cities I like better. Neuschwanstein is a ways out of Munich so either sign up with a tour or make arrangements ahead.
If you're leaving back out of MUC, the S-Bahn (Suburban train) is a good ride back out to the airport.
Check with your bank and make sure your ATM card works over there. Most do, some require a notification to the bank. Take some US currency with you - I've only (nearly) been burned once with an ATM card: that was a day I arrived in France when the telecom workers went on strike and shut down the ATM networks. Fortunately, I was able to get cash at an AmEx office. Now I carry some cash, usually left over from a prior trip. LIkewise, notify your credit card company in advance.
There are still some places that won't take credit cards. Not many, but a few. So carry some cash. Some places will also not be happy about your US credit card - the cards in Europe are generally Chip & PIN (meaning they have an imbedded chip), while the US cards are magnetic stripe. I've run across a few places that didn't know how to handle the mag-stripe cards.... which is why I carry cash, too.
I'd also add to Scott's comment that if you can get an unlocked phone, look at some of the international prepaid SIM cards, such as those Telestial sells. The only trouble with a local SIM (and I DO use local SIMs for data....) is that many of them charge high roaming fees once you go into another country. If you have an iPhone/iPad, shut off data service befor you arrive. Data is super expensive to roam.
Wont have a car, mostly trains/cabs.
Assuming you're flying into Paris & leaving from Munich, you will probably not find a rail pass to be cheaper than just buying a one-way ticket. In Europe, for the long-distance trains you need both a ticket and reservations on a particular train.
My favorite auto rental group is AutoEurope - it's US based, very reliable, and often has much better prices than you can find elsewhere... and significantly less than a walk-up rental. They also have a link from their site to raileurope (autoeurope.raileurope.com), which I have also found to be decent for train schedules. I've even been known to make an autoeurope booking via their website when I was in Europe already.