My partner and I spent 21 days in southern Germany a few years ago. I'm pretty good at traveling economically, so my experience should be a lower end estimate.
I like to to express my results in euro, not dollars, because I've found the prices in euro to be pretty stable, whereas the dollar to euro exchange rate fluctuates. You can convert this to dollars at the current rate. I also like to express it in nights because the first and last day usually add up to one day, so the number of whole days is the same as nights.
I'm not going to include my expense for seven nights in an apartment in a small town, because most people don't use apartments and if you don't do that, it's unrealistically low. I'm also not including four nights in Munich, where expenses are maybe 20% higher than in small towns. So for the other 10 mights in small towns in southern Germany, we spent about 135 euro per night. That was food, lodging, and transportation for two people, double occupancy. At the exchange rate in effect then, it was $182; it would be less today. Breaking it down, we spent 72,30€/nt for accommodations (with breakfast) 37,43€/nt for food,, and 24,10€/nt for travel.
You probably can't get that low. I get all of my accommodations from town website, which is the least expensive way, and I eat traditional cuisine in local restaurants. I also know the transportation system in Bavaria very well and can take advantage of the best price. But it gives you a minimum to start with.
But if you plan well ahead of time, you can figure most of this out yourself. Book rooms, and you'll know the cost of accommodations. Look up transportation prices on the Bahn website. For meals, I have consistently spent 20€/night/person, average. A good estimate for you might be 30€/pers/nt.
Good luck!