I'm 43 and have been doing yoshinkan for about 8 years or so. The soreness will definately get better as you improve, especially your breakfalls. I'll second the recommendation for glucosomine. Do you mind if I ask who your teacher is as a point of reference? I also have knee problems, and my instructor is very understanding, even allowing me to stand if needed during periods where the class is in seiza for a long time. I talked with him about the knee problems I was having, and he helped me to work through them. I think your instructor will do the same if you give him the opportunity. Yoshinkan is kind of known for its severe training, but I think allowances are usually made for individual situations (as long as you aren't thinking of the senshusei course in Tokyo...
).
Stick with it, learn to relax, stretch and breathe as much as possible BEFORE class.
Best of luck and good keiko,
Ron