Take the RE 1 at 9:04 to Ingolstadt and transfer there to the continuing RE 1 to Nuremberg and you will get there by 10:50. If you wait for the 9:26 RB 16, which is direct, you will not get there until 12:15 because it makes 27 stops along the way. Although the Regio-Ticket Munich-Nuremberg is 3 EUR cheaper than the 59 EUR Bayern Ticket, the Bayern Ticket will give you free public transportation in Nuremberg for the rest of the day.
The Munich-Salzburg regional train leaves the Hbf at 55 or 56 past the hour, so you would have to take the 9:55, However, if each of you buys a 3.90 EUR MVV ticket, you can use that in addition to the Bayern Ticket. The train will stop at Munich Ostbahnhof at 9:03, then the Bayern Ticket will be valid for the rest of the day. Or if you are elsewhere in Munich, use public transport to Ostbahnhof and get the train there.