Cow's milk protein allergy or intolerance is often referred to as MPI, Milk Protein Intolerance. Most babies who have this also cannot tolerate soy so it's called MSPI, Milk/Soy Protein Intolerance. They don't usually refer to it as an allergy because it cannot be tested through an allergy test.
My son had eczema and it would get worse and worse. He also had a constant runny nose/congestion, super crankiness, tired, etc. However waking after 45min is a VERY common thing for a lot of babies. It has to do with their sleep cycle. My son would wake up several times a night due to the itchiness that came with his eczema.
My son didn't have any problems with the formulas. He tried the Alimentum and eventually the Neocate. Taste-wise he didn't seem to care. If you add it slowly he probably won't notice. I would eliminate the dairy first from your diet. Takes a few weeks for it all to leave their system though to see if anything improves. If still nothing I would suggest then eliminating soy. And don't forget all the hidden dairy/soy under different names in many processed foods, such as in breads. If you did both and after a few weeks still nothing then I would think it had nothing to do with the milk or soy.