Hi, I have a son who is now 15 but was diagnosed with Crohn's at 12. Reading your story sounds a lot like my son at your son's age. Very picky with food, mostly just soy formula until 2...would not eat regular food. Never could get a jar of baby food down. No bouts of constipation but bouts of unexplained diarrhea (crohn's can present with either), random vomiting with no apparent sickness, always small for age... Testing showed no parasites, wheat or milk allergies.
We went the reflux route for several years, not real successful. He wore the same shoe and clothes size from 3rd through 6 grade. In 6th grade was diagnosed after several months of nausea, then increasing periods of diarrhea to severe vomiting and diarrhea. I do believe he had crohns as a baby. Maybe not, but looking back, I see a lot of symptoms along the way.
There is a good parent support group on line for parents with several parents of small children. It is dragonpack.com . Even if you just have questions about the process of diagnosis or symptoms they can help. In order to post you do need to register and it may take a day to get access but in the meantime you can read anything on the site. I would really recommend you visit this site.