Found this site while panicking about getting from Salzburg to Munich a week ago. I didn't use the info here in the end but held the number 24 bus route as a good back up .
I ended up using Meinfernbus (http://meinfernbus.de/en) which is similar to Megabus in the UK or maybe the greyhound service in the USA (?).
One bus, from a stand just behind the train station in Salzburg (opposite side of the train station from the bus station - just walk all the way through the train station and come out the other side). Bus took about 3 hours, due to queues for passport checks on the road into Germany and roadworks on the road but it was just the one bus with no changing or walking to do.
I had to book a ticket in advance, but was able to do this easily on my mobile phone and used a .pdf version of the ticket on my phone which I was able to download. Cost was 7 euros.
No fuss, no hassle, no walking (in the rain)!
Good luck all!