Guess I forgot to update. Sorry!
The results from his procedures (endoscope and colonoscopy) were totally normal. They had decided to switch his formula to Nutramigen before the surgeries, and low and behold, that was the key to him gaining weight. While I'm happy that we know for sure nothing is wrong with him internally, at the same time, I'm kind of upset that they didn't try to switch the formula before he had to go through those procedures. We were released from our specialist and have been seeing our regular pedi since the follow-up appointment.
Since then, he's been great. He's nearing one now

(January 31st), and I'm scared to death of trying actual milk. We're really not sure if he has a milk 'intolerance' or a milk 'allergy'. We're waiting to do milk until his one year appointment after a talk with the pedi. He does cheese fine. Yogurt is a bit touch-and-go. Sometimes it makes him sick, sometimes not.
I'll be back to update after his year appointment with the pedi. It'll be interesting to see how much he's gained. He still gains on the slow end, and I'm a nervous wreck every time we get near that scale!
I'm so glad that you guys finally have a diagnosis for Danny. That had to take a lot of weight off of your shoulders. How's he doing?