In the past, when I was just passing through Salzburg to get to other places in Austria, I've arrived at MUC and immediately taken the S8 and the regional BRB to Freilassing, which is right across the river, in Germany, from Salzburg. I never had a problem with late arrival at MUC or the trains not being on time (the BRB runs hourly). If the hotel in Freilassing had not closed, I would do it again.
However, you might want to stay closer to MUC the first night. I like Freising, and, in good weather, it's fun to sit out in the Biergarten at Weihenstephan and have dinner. As Russ says, there is a regional train connection from MUC to Freising that takes about 12 minutes. However, that train runs only once an hour. Every 10 minutes there is a bus leaving MUC for Freising and the trip takes 22 minutes. They both go to the same place, Freising Bahnhof. So, unless the train is leaving imminently, take the bus, you'll get to Freising sooner.
In the morning, take the direct S1 from Freising Bahnhof to Ost Bahnhof. It takes 50 minutes. There are a few faster connections (44 to 46 minutes), but they have connections and only occur once an hour or less, so your most consistent connection would be the S1. Or, if you are taking one of the hourly trains that leaves first from the Hauptbahnhof you might want to get off there from the S1.
However, although there are things to do in Freising, with jetlag, you might not want to avail yourself of them. It only takes 30 minutes to get to Ostbahnhof by S8, and there are some Marriot hotels about a ¼ mile up the street to the NE of Ost.
As for the train to Salzburg, I've always taken the regional BRB. Everyone I've been on in the last 10 or so years has been a very modern, double-deck train with lot of space. Travel times are similar for all of the Ost-Salzburg trains and the BRB, with a Bayern-Ticket, is much more economical.
I would also not spend the extra money for 1st class. As a business traveler in the 1980s, on the company dime so to speak, I always went 1st class. I thought 2nd class was beneath me. Once I tried 2nd class, I decided 1st class was a waste of money. 2nd class is perfectly comfortable, just as fast, and maybe more interesting. The last time I rode in 1st class, I was the only person in the entire coach.
