You get out what you put in
There are going to be classes where you'll think that if you hit the mat one more time there is no possible way you're going to get back to your feet. There will also be classes where you are going to worry about cooling down too much between techniques. The truth of it is that you'll get out of it as much as you put into it. You obviously have an idea of what you need in terms of physical fitness, so the trick becomes not letting yourself give in when you're coming to the end of your endurance, or you're a bit sore.
Regardless of the activity, just when I'm about to give up I always tell myself that only just RIGHT THEN, did I start to grow... because right then I reached the limit of what I could do comfortably, and where is the resistance in that? When I'm ready to give up I'm stretching not only what my body had done before, but also what my mind thinks it can handle. In aikido that means hitting the mat again and forcing yourself to get up.
And I can tell you, my aikido gets me to that point more often and faster than my TKD training does - as counter-intuitive as that sounds. You won't regret it if you start training, IMHO.