We have visited all the places you mentioned, since we lived in Augsburg, Germany for four years.
We visited the Oktoberfest three times, taking the train down to Munich from Augsburg. Hotel rooms are hard to find during the fest. It sounds like you already have a hotel booked. If not, then book it ASAP.
We enjoyed the fest and the atmosphere with the music and singing. The beer is great as well. Try to see the Oktoberfest parade with the old beer wagons pulled by horses and people dressed up in traditional Bavarian clothing.
Pace your self with the beer. Mugs of beer are liter sized and the alcohol content is higher than US beer. Try to go before evening when it is not as crowded, but stay for the music and when the tents start swaying with all the singing. You will probably want to sing along as well. Roasted Chicken is a favorite dish during the fest, and of course the bratwurst and kraut.
Regarding the rest of your trip, both Krakow and Prague are great places to visit. Both are worth about three days in my opinion. If you can swing a visit to Auschwitz, west of Krakow, it is something dreadful to see were genocide occurred, but important to understand the history.
If you have time, take side trips to Salzburg, Austria (and nearby Berchtesgaden, Germany), as well as Garmisch and Fussen for the Zugspitze and castles.
