Well DS1 has just turned 4 and we've been in the same boat as you, though DS1 is lactose intolerant. He was on losec til he found his feet and we slowly weaned him off but then had to go back to it for abit and wean him off again so he was closer to 2 by the time he was losec free. We took our time and just lowered the dosage every 6 weeks or so by a tiny amount then gave his body time to adjust. I'd be inclined to wait til hes on his feet before you try again.
Sounds like your DS has more than an intolerance, it sounds like hes totally allergic so the tests may pick it up. We found that because DS1 was 100% lactosefree that the tests weren't bringing back accurate results because since it wasn't in his system at all he wasn't having the same reactions to the introduced stuff - make sense much?? He was older when we had tests and IMO keeping his system protected helped it heal itself abit so he grew more of a tolerance to tiny amounts. When we put him back on dairy and lactose his body spun out though and the tests were really clear. Even at 4 he can cope with a certain amount then its suddenly too much and we get the reflux, the sore tummy, vomiting, etc.
At 9mo we also went through a stage with both boys where they just got super unsettled so that may be whats going on with your boy. Might not have anything to do with reflux, it might just be that stage! Hope so
Not sure if any of this helps lol but thats our experience anyway!