I just booked a similar trip, in reverse. I am arriving in Budapest and then travelling by train from there to Vienna. From Vienna, I will travel by train to Prague. From Prague, I have a private shuttle booked to Cesky Krumlov and from there to Salzburg the next day. Then I will take the train from Salzburg to Munich and fly home from Munich.
I have booked first class train tickets with seat reservations for those three train trips at less than half the cost of a rail pass. In addition, by booking through the countries' rail websites, I had access to many more options (time-wise) than the Rail Europe site showed. (Individual tickets through the Rail Europe site were also a little more expensive.)
That worked best for us, since we are travelling at what I expect will be a busy time and have booked our accommodations in advance, as well, so we know our exact travel dates.
Had a rail pass been even close to the cost of booking individual tickets, I would have considered it, but there was no contest.
If I recall correctly, most of the sites allow you to purchase 90 days in advance, but at the Hungarian rail site it's 60 days, I think. However, I guess this wouldn't affect you, since you will be travelling into Hungary by train, not out of Hungary, so you would book at the site for your departure country, anyhow.