H.S.
If it goes back up, take your son to a hospital that has a pediatric emergency room. If it stays around 99.9, that's considered a low grade fever and I would consult with your doctor. Any time your son has a fever of 104, get him to the ER as fast as you can and call your child's doctor to let them know where you are going. 104-105 is where the brain starts to die which can cause brain damage. A fever this high for such a long period of time can indicate something other than Pneumonia. When I was a baby, I kept spiking high fevers and was really sick and my doctor just told my mom (for 2 months) that it was a cold and finally, she stopped believing him and took me to Mott's Children's Hospital where I was diagnosed with severe Pneumonia and was in the PICU for almost a week while the doctors got me stabilized; had she waited another 24 hours, she would have been burying me.
Follow your instincts! I hope your little one feels better and I wish you luck.