I think if you don't have any bad reactions on the start up phase then you will eventually reach your max maintenance dose in about 8-12 weeks. Since you have reactions i guess you will maintain a lower dose until you get over it and go higher dose and eventually reach the max dose. Do you take anti histamine before receiving the injection?
I had gastric reflux too but i don't have any known food allergy. I have no h pylori infection too, most people with reflux had it, i wish i had it as it can be easily cured with antibiotics. Have you heard of ALCAT food test? I'm tempted to try it but doubting the accuracy.
If antihistamines helps then i think you can take them when needed, most people feel sleepy with antihistamines so it's just normal. It's effect last a day or two so maybe you could take it at night.