I'm not seeing a direct train from Munich to Prague running currently. It looks like the direct trains return on Tues., Sept. 11.
Prior to Sept. 11 there is a 3 change connection using an RE to Ingolstadt, an AG to Regensburg, and 2 ALX trains with a dedicated change in Schwandorf. The change in Ingolstadt is 13 minutes, one or two platforms. The change in Regensburg in only 4 minutes, one platform. The change in Schwandorf if a 10 minute, same platform change. I don't see the Prag-Spezial ticket available online for this multi-train connection, but I think you can still purchase it at the station with a surcharge (or maybe from a ticket automat or on the Bahn store).
Starting Sept. 11, the direct train runs every two hours from 6:42 to 16:44.
The 38€ price is for a "Prag-Spezial one way" ticket. It's the price per person. It doesn't go up as lower cost tickets sell out, like the "Savings Fare" tickets; that is always the price, but it appears to be non-refundable. There is no time limitation (like after 9 AM).
You can also get to Pilsen from Munich (or anywhere in Bavaria) using a Bayern-Böhmen-Ticket (28€ first person, 6,60€ each next 4 people), which is like a Bayern-Ticket (starts after 9 AM workdays) except it includes a part of the Czech Republic along the border with Bavaria.
The Bayern-Böhmen-Ticket gets you to Pilsen; you must purchase a Czech ticket from Pilsen to Prag. That fare is 105 Kc (about 4€). You could get off the ALX train in Pilsen, buy the ticket at the station, then spend time in Pilsen before continuing on to Prague on the next ALX or Czech train (although Czech trains are old and dumpy). Or you could buy it online from www.cd.cz. I think you could buy it on the train from the conductor (anyone know for sure?).
If you are traveling to Prague on a weekend day, the Bayern-Böhmen-Ticket will cover you on any train, even the 6:42 or 8:43 ALX. If you are traveling on a weekday and want to use the 8:43 ALX, you can't use the B-B-Ticket until after 9 AM. The 8:43 train stops at Freising and leaves there after 9, so you would need an additional 8,70€ MVV ticket from the Hbf to Freising, so it would be cheaper with the Prag-Spezial-Ticket. However, if you are flying into MUC on a weekday and want to go directly to Prague that day, you are free with the B-B-Ticket to take any ALX train except the the 6:42. There are buses (2,90€) from the airport to Freising Bhf every 20 minutes, and the 8:43 leaves Freising after 9.