A nice trip to some of my favorite places. Trains are indeed the way to go. The pass option Laura outlines will cost $390 for two. But it's not necessarily the way to go. Maybe just some tickets...
MUC - Salzburg, €28 (Länder Ticket)
Salzburg - Munich, €28 (Länder Ticket)
Munich - Bacharach, €49 - €100 (DB saver fare)
Bacharach - Bruges, €78 (DB saver fare)
Bruges - Brussels, €14 x 2 = €28 (standard ticket)
All that works bout to about €210 - €260 or ($225 - $280 at current rates) for two. So you'll see some substantial savings this way.
An additional day trip from Bacharach on a Länder Ticket costs €28 or less. I agree with Jenny on Marksburg. She picked a good one for her first experience.
The saver fares need to be pre-booked. The other tickets can be bought as you go in Germany and Belgium.
A pass is helpful if you need flexibility of travel date/time - the two DB saver fares are not flexible meaning you must travel on the dates at the times you schedule when you book. It looks like your itinerary is very firm, however, and that sticking with a saver fare ticket won't be a problem. Buy them well in advance for the best prices - which will rise as tickets sell.
If you do a cruise, don't get on the boat in Bacharach, or you'll be on for only 40 minutes. Take the train south to Bingen to board and cruise north to St. Goar to see the best part - takes about 1.5 hours.