We do get into Munich early morning (9:45 am), the day before the
tour. We planned on arriving in Munich, take the train to Fussen and
go to the room- maybe walk around the square a bit just to grab a bite
to eat. Nothing else that day.
To me, the hard part of your idea is all of Day 1. If you arrive roughly on time, you could probably get through security and passport control and baggage and take care of personal stuff (ATM, food/drink/train tickets/ etc.) and to the station for the 11:51 departure from MUC to Fuessen (a 3-hour train trip) and arrive by 15:00, then transit to hotel and check in. Any jet lag and you should be feeling fully flogged at this point. At the most you'll have time and energy for, as you said, a brief walk-around, a meal, etc. but will likely not be ready to sightsee or investigate the town.
Whether it will happen as scheduled is hard to say. Whether that's doable for you is hard to say as well. I only know that several of my flights have been delayed by 45+ minutes or longer, that location of arrival gates matters a LOT once I'm off the plane, and that even if everything goes super-smoothly, I'm not feeling at all refreshed and energetic after such a long sit. If I have to transit anywhere else from the airport, I want it to be REALLY close.
Day 2 sounds doable if you do the tour early. You will have to get back down the hill, to the shuttle bus, and to Fuessen promptly to fetch your bags, have some lunch, and get on the 13:05 train for Munich in order to make your 4 pm tour meeting.
To me the question is not only whether the outing is doable, but whether it's reasonable to invest so much time, cash, and scurrying around into just this one thing - a 30-minute tour of N'stein.
Should we reconsider?... Is that doable?
Would Nymphenburg and perhaps another sight or two in Munich, something your tour doesn't include, be more reasonable, more relaxing after a long flight, more rewarding? Does your original plan match up to the alternatives? You probably have a hunch what I think already. Yep. It's the tourist's dilemma - with no experience in any of these places, you have to find answers yourself, somehow.