If you want to do this trip cheaply, using an auto is the wrong way to do it. The German railroad will take you to most of the places you want to visit and at a cost far lower than auto rental, fuel purchase, parking costs, etc.
The railroad offers tickets, for example, that will cover a good deal of your trip at €26 for one day of unlimited travel for two people - thus €13 each.
Secondly, going to Munich for the Oktoberfest could be tricky. Many hotels are probably already booked and those that have rooms available will nearly double the cost of the room. If you really want to go there then, you'd be wise to look for a hotel outside the city.
Do either of you speak any German?