Hi Vikki,
I'm sure when you get your gg-grandfather's records it will be much clearer why he left the service, was he injured or his enlistment up.
Some things to consider while you wait for those things are the following. He was over 40 years old, and even though he may have been in good physical health when he entered the service, the nature of the cavalry broke a mans body down. When issued his first equipment he would have drawn over 70 pounds of gear to strap on to his horse, and his own body. Even though he would have figured out what he truly needed to carry, the weight on his body would have still been there. He would have had a pistol, carbine, saber, cartridge box full of ammunition strapped around his waist, moving around as he rode his horse. I can't even begin to imagine all the potential health issues that would cause. I do know many troopers suffered from intestinal disorders. He would have had to contend with bad water, marginal food at times, as well as some diseases he wouldn't have found at home. His personal health could have been effected by some of these things. If you have never been to Vicksburg MS and want to get a feel for what your ancestor may have experienced, visit the National Battlefield Park there. It is a wonderful site to visit. If you want to get a real sense of what it would have been like for him, go in late June. If you have never been in Ms or the deep south during the summer, its a treat. There are many other factors that could have effected his leaving the service; he may not have been home for three years, his wife may have been struggling with the farm at home...... very many things to consider. As a historian, whether family or otherwise, I think we always want to know why.
If you are not familiar with what his uniform would have looked like check out this site:

http://civilwar.ilgenweb.net/photos/regimentindex.html there are members of his regiment on it. Good luck with all your searches, if you already know this info, hope you didn't mind seeing it again.
bg