Food Allergies Treatment

My appologies if this is long winded and difficult to read…
My son is 4 months. He was breast fed for five weeks and he never really got into it, so i started him on SMA Gold. He got very constipated, sick and generally miserable. So after lots of doctors saying to give him something to releave the constipation, and gaviscon to stop reflux, he had very mucousy, bloody stools. So finally, at 7 weeks of age, he was diagnosed with Lactose Intollerance. I didn’t take the diagnoses lightly, and asked a few medical professionals and they all said the same thing. So he was started on Nutramigen and that was that. He seemed to get better. The blood in his stools stopped, and he had no reflux and he seemed happier.
Then four weeks ago the bloody mucousy stools started up again. I returned to the doctor who took a stool sample and sent it away. It came back NO infection. Both my GP’s were stumped, so they decided to refer me to the hospital to see a specialist. But two days later, he refused to feed! He became irritable, started arching his back, pushing away from the bottle, screaming at me, not wanting to be held. The only way he’d go to sleep was on his own on his back or stomach. So i took him to the hospital after he went a full day without eating anything, and we stayed in all weekend. They tested his poo (positive for blood, no infection) his blood (all fine) and all the normal stuff like heart rate etc and he seemed fine, but still didn’t feed normally, and when he did have something he’d scream at me. So the doctors decided to switch formulas to Neocate LCP and to give him ranitidine and gaviscon. Now, here’s my problem and question. We were discharged with the Neocate and the gaviscon and ranitidine, and they said that they suspected he had a bit of reflux because he wasn’t feeding, and that they thought he had cows milk protien allergy and NOT lactose intollerance. But what i don’t get is Nutramigen WAS a cows milk free formula, they’ve just put on him on a more refined type of formula (it’s the most easily digested formula you can get!) and he had NO reflux before I went into the hospital. Since getting home he has no visible blood in his stools (but this happened when we started him on the Nutramigen) but he’s still only having the max of 4 ounces every four hours, he’s still fussing but he does seem a bit better.
I was wondering if there’s anything else he could have that’s NOT cows milk allergy that would account for all the symptoms? Any other mothers out there had an experience like this and what did you do? It’s just something doesn’t feel right to me and I don’t understand the switching of the formula when it was already cows milk free. Also, if it is cows milk allergy, then why isn’t he feeding properly now (almost a week after being started on the Neocate.)

I switched from cow’s milk to soy milk several months ago. Recently I’ve started breaking out in hives after my daily breakfast of cereal and soy milk, although I have no reaction to other soy products (tofu, soynut butter, etc.) Is there any reason I would be allergic to just soy milk?