My son had a lot of food sensitivities; he never broke out into a rash or anything, he'd just roll around in his crib and wake up frequently at night. You might also have a LO who has tummy issues -- not full out allergies, just sensitivities. If that's so, then you've got a tough row to hoe!
I'd keep at the HTTJ thing. A lot of moms find it takes 2 weeks before it works. There may be some success stickies somewhere; I'll try to hunt them down. In the meantime I strongly urge you to check out our FAQ section here and in the Naps and General Sleep Forums. You migth find something there that rings a bell.