Hang in there, FranG... it does get better. Like the others have said, once you're able to find the right medications for your son, things can improve dramatically. It took two years of trial and error (mostly waiting for meds to work or fail), but now my son is on Remicade and only thinks about Crohn's on infusion days. On the days in between, he's living a normal teenage life, going to school, playing sports and planning for his future.
For the "off" weeks of stomach aches, nausea, etc. I guess I just focus on getting through the day and hope for better tomorrow. It sounds like your son might just be fighting through a virus with the symptoms you listed? Try not to let normal life things, and colds and viruses are normal life things, get you down. They'll pass.
Hugs to you and be sure to take some time for you. Do something for yourself that allows you time to breathe.