Help with German train decision, please

2nd class seat reservations have to be purchased separately from the ticket, either when you book your ticket, or independently. Obviously for the flexible ticket you can't reserve seat until you decide on the train, but you could do it at the station before you board. For the saver fare there should be no problem in getting reserved seats.

Note: Many people squat in seats that they have not reserved, even quite prosperous looking folks - Very politely but persistently showing one's reserved seat receipt has always worked for me. All seats are numbered. Reserved seats are usually (when things are working right) designated by lighted signs above the windows or by paper labels in slots above the windows. "Fenster" means window seat, "Gang" means aisle seat. Usually they even have a picture of the window with the seat number.

https://www.bahn.de/en/view/offers/other/seat-reservation.shtml?dbkanal_007=L04_S02_D002_KIN0060_NAVIGATION-LINKS-SITZPLATZRESERVIERUNG_LZ01

There is always the chance that you won’t get a seat, but usually that won’t last for the entire trip.

See if your airline participates in the Fly and rail program.

You can take a fast train as long as you pay the fare.

It is always a gamble in buying a train ticket in advance because your plane might be late. When i did that, my plane was several hours late. However, early fares are usually very low and it may be worth the gamble to hope the 39E fare works and saves you a 105E fare.

"If I did the research correctly, this combination is cheaper than the German Rail Pass 4 day "twin" rate."

Sounds like you have compared 2 days of travel with 4 days of travel, which is not comparable. If you have future rail days planned after arrival in Munich, you should add the separate cost for those days to the 2 days of tickets you have already added up.

The rail pass certainly frees up Day 1.

Thanks so much to all who replied! I somehow missed that we would need seat reservations once we decided which train. After reading more, I understand we can do that at a kiosk or a ticket counter in the Frankfurt airport train station. I think we will stick with the plan of purchasing flexible tickets from Frankfurt to Gengenbach so we don't have to worry about what time the plane gets in and how long it takes to get through customs and luggage. Then for the trip from Gengenbach to Munich, we will do the saver since we will be controlling our time. Our carrier (United) is listed as participating in the Air to Rail program but I could not find it anywhere on their website. We've already bought our tickets so it is probably too late, anyway. But, will remember for future travel.

My understanding on the rail pass is that it is for X consecutive days; therefore, since we needed it on Day 1 and Day 4, we would need a 4-day pass, not a 2-day. Our day 2 is on regional trains using KONUS and our day 3 is a guided tour in a private vehicle. Once we arrive in Munich, our tour operator handles all transportation. So, the two individual point-to-point tickets seem best.

Our carrier (United) is listed as participating in the Air to Rail program

"Air Rail" (aka "Express Rail", Lufthansa) is a different concept from "Rail&Fly" (Deutsche Bahn) which United is participating in. Somehow they are eager to hide it from their web site but I had success once by calling them.

"My understanding on the rail pass is that it is for X consecutive days..."

That's one of two options. The more common choice is the flexi pass where you buy 3, 4, 5, 7, 10 or 15 days to use within a month's time.

If you have no additional planned train journeys in Germany, then a rail pass isn't going to be a good deal for you.