Garmisch was not all that badly affected by floods. Right now the trail through the Partnachklamm is closed as a lot of debris clogs the gorge and some other hiking trails may be washed out. It is always a good idea to enquire about conditions at the tourist office before hiking into the mountains. But other than that it is business as usual in the area.
You can plan your train trips (or rather: all trips with public transportation) at www.bahn.com, the website of the German national railway.
Trains from Munich to GaPa go at least hourly, though I think there are currently trackworks along the way, so you will probably have to change to buses between Weilheim and Murnau. Just follow the crowd. The trip can be covered with a dayticket called Regio-Ticket Werdenfels. It costs 30 EUR for 2 and covers all S-Bahn and regional trains in Munich and to GaPa. You can buy it from any ticket machine in Munich, incl those at the airport.