The shoulders has already caught up with me, I had 2 shoulder surgeries due to many dislocations, mostly in the water. I feel like I have that under control however with all the stretching and foam rolling I do. I'm going on 2 years post op and my shoulders feel healthier, stronger, and in better shape than ever. I'm 23 so in some ways I guess I was fortunate to learn young to treat my shoulders right. The marathon sessions aren't really treating them right though.
I like your idea of the short sessions, which I will be using this winter when I'm traveling in Central America. No need to marathon when the surf isn't going anywhere and you don't have to work! (Treating myself to some post-college traveling before I grow up)
I've been experimenting with yoga lately and I pretty much agree with you, takes up too much time for not a ton of benefit. Although I have learned some stretches I like. Time much better spent doing Inside-Out/Magnificent Mobility stuff and foam roll+ specific static stretches. Foam rolling the lats after a marathon session is crazy, hurts so good.
The balance training is interesting. The only balance type stuff that I feel like has helped my surfing is skateboarding and maybe the single leg work. I cannot do indo boards or swiss ball or anything like at all but I surf fairly well for an east coast guy.