T.H.
My son had a bad milk intolerance when he was an infant but (thankfully!) grew out of by a year. The kicker to knowing I think is the gas issue...does he have wickedly horrible gas? If so, then it's probably a milk issue. My son was only a few weeks old and would literally clear a room with one toot! He also had a full body rash. It was everywhere, and the cradle cap didn't really go away either. I figured it out when he was probably 2 months old, just from looking at the symptoms and talking with a friend who's daughter had a milk allergy. I called my pediatrician and immediately put him on soy formula. He actually had been on a lower lactose formula, Enfamil of some kind, but once I put him on soy I started noticing changes very quickly.
If you aren't noticing the smelly gas issues I'd probably say it might be GERD. Make sure his doctor knows how often and how much he's been spitting up, perhaps putting him on a prescription might help.
Good luck!