Hi N. - this is C.! Nicolas (now 3) had exactly the same thing at about 3 months. The pediatrician and pediatric gastrointerologist (spelling?) said it was a sensitivity to cow's milk protein. I cut out dairy and he really improved, but still occasionally had blood in his stool and would projectile spit up after I ate corn or certain legumes (soy, garbanzos). I eliminated those two and he had no more problems. He doesn't get the tummy problems anymore with dairy or corn (he can eat legumes without problem now), but he just becomes the crazed energizer bunny in the middle of the night and will not sleep. Needless to say, we still avoid corn and dairy. I haven't really tried either in about a year, so I don't know if he has outgrown it. The problem is now he will not eat dairy even if I tell him it won't hurt him. He won't even eat butter on bread.
It may be that the nursing problems are related to some other food sensitivity. I was lucky to be able to correlate projectile spitting up and crying at the breast with corn products. The docs didn't believe me on the corn, but as soon as I cut it out, he was fine.
I did use that Nutramigen a little bit, but he hated it. I'd try eliminating some other potential problem foods for awhile and see how he does.
When he gets older, we do enriched rice milk and OJ with calcium. Plus, I am fortunate that Nicolas loves Brisling sardines which have calcium and vitamin A and D.
One thing to watch out for is tooth decay. I suspect that because Nicolas may not have gotten enough calcium and vitamins A and D, his enamel is weak and he got cavities. I'm sure it didn't help that I night nursed him for a really long time, but there are plenty of babies who do night nurse as long who didn't get them. Just something to watch out for once he gets some teeth. I wouldn't night wean just for that, but you might take a second to wipe his teeth with a soft cloth afterward.
I don't know if you are as much as a cheese addict as I was, but if you are suffering the loss of cheese, it will get better. I don't miss it much anymore. It just means I eat a lot of carne adovado burritos instead of enchiladas anymore. Also, coconut milk ice cream is a reasonable substitute. Whole Soy & Co. makes edible soy yogurt. Any other brand I find inedible.
Sorry for the long, rambling post, but we have been there, and actually still are there.
Best,
C.