I had taken practice rolls with this same lens combination (Elmarit 90mm 2.8) for months before the trip and there were never any issues. My best guess as to what happened was that something got worked loose while in the airplane overhead. This was the first time my M-A was on a plane. I feared the worse, but was confident that my lens was alright. I salvaged the trip by sticking to my other cameras and only using the Leica at infinity, where I was sure to nail critical focus.
While my shots taken in the valley turned out fine, I had the task of root causing my focus issue. Being brand new to Leica, my only other lens was an Industar 50mm. So I threw it on a screw mount adapter and tried it out. Confirming my suspicion, the Industar was off by the same amount, in the same direction. Just to confirm one last time, I remounted the 90mm and checked each focus distance and it appeared that the lens was back focusing consistently.
With this knowledge, I knew that this would be the one adjustment I could comfortably perform on my own. This is the infinity adjustment, shown below, looking like a car cigarette lighter with an Allen bolt in the center. To my surprise, this new Leica M-A uses an Allen head instead of a flat head. This makes it much easier to get a tool through the mounting flange to adjust.
I was able, through trial and error, to rotate the bumper in just the right amount (less than a few degrees) to nail focus at all distances.
The TYP-127 has been on multiple trips since the repair, including flights and back county hiking. I haven't had any issues since. It seems like the camera was just settling in. While this is extremely concerning for a rig this expensive, I guess these type of issues are the price of admission with an all mechanical camera. I was very lucky this wasn't something internal or it would have been making a trip to Germany, alone.