Definitely keep an eye on the cough -- Coughing after exercise can be a symptom of exercise-induced asthma, as I learned from personal experience. I now use an inhaler, and it has made a huge difference in my breathing when I ride.
As for the toes, I used to have that problem too. For me, the solution was two-fold . . . I went to a size larger shoe so that I had room to wiggle my toes during a long ride, and I put pads (Dr. Scholls or something) in the shoe at the ball of the foot to reduce the effect of vibration.