OP here. Thanks, everyone! 12:40, yes, I posted in Special Needs several months ago -- good memory!
12:37, thanks for the perspective on allergies. How did you find out your DC had the allergy to corn? I actually had wondered if corn might be an issue with my DS because he got worse on the Neocate and because I had a bad reaction to corn while pregnant (nausea at the thought of eating it).
The ped is doing stool samples and sent us to have blood drawn to test for a bunch of things, including allergies (although I'm not exactly sure how that works -- I thought you needed to do a skin test or something??).
We got an appointment with Children's GI for a second opinion, but we can't get in until the middle of Feb. Our ped said to emphasize it was a second opinion so they looked at it more closely than a first-time visit.
12:43, he has always had some difficulties, but it's gotten worse since early December. I thought about a blockage, too, but I think it's probably something that's been going on all along.
12:40, I will look into the geneticist as an option. It's scary when you google "metabolic problem."

Hopefully there would be something in blood tests that might suggest a need to look further into this avenue?
I think one of the major problems in getting people to look into this has been that my DS is actually quite healthy, gaining weight fine, no motor issues, etc. He is tired a lot and therefore not very social, which worries me, but our ped thinks he is just uncomfortable and will be more social when he feels better. I do think tiredness plays a part in his behavior a lot of the time, but his tummy seems to cause the tiredness.
I have debated how far to pursue this if he is healthy physically, but I do think that the sleep deprivation is starting to interfere with his ability to socialize, and I think he would be a much happier kid (and we would be saner parents!) if we could get this worked out.
Honestly, I suspect we might not get a solution, but an answer of some type might be helpful so we at least know what's going on.
Thank you all! If/when we ever figure this out, I will let you know!