What a wise physician you have! He was able to connect your son's physical symptoms with his emotional state. I hope you and your son will continue to have regular visits with this doctor so he (or she) can evaluate your son's progress.
First, you must do a little reading and research on homeschooling. Fortunately, FamilyEducation.com has a great selection of articles and resources to get you started. First, visit our How to Homeschool center.
Next, read Linda Dobson's book, The Homeschooling Book of Answers or The Complete Idiot's Guide to Homeschooling by Marsha Ransome. Both will help you learn about homeschooling.