Your gradual transition is wise. Babies will have different stools on different kinds of feeds. His current stooling sounds a little more like breastfed stools, actually. The gas IS a concern but as long as he’s happy, the rashes are gone, and weight gain stays close to his own natural course, he’s good to go with this new formula.
My first guess about the gas is that it’s from the lactose, which is present in his new formula but was not in the Alimentum. Lactose is the natural baby sugar found in nearly all mammal milks and is health-protective. True inability to digest lactose (lactase enzyme deficiency) is incredibly rare in babies, as children are designed to thrive on mommy milk. However, intestines that are irritated by food reactions or infections can temporarily lose good lactase production. This will lead to gas and some loosening of the stools, as natural flora do their best to digest (ferment) for baby what baby’s own enzymes failed to handle. Baby will absorb some of the lactose break-down products provided by the flora. Over time, recovering intestines will return to good lactase enzyme production and gas will diminish.
If this IS the right formula for your baby, the gas should gradually decrease, the spitting up and rashes should not return, and your baby should otherwise be mostly happy, and thriving. If only gas proves to be a continuing problem, I would have a slight concern that baby is not digesting and absorbing as much sugar as would be optimal. Sugar is important for brain development. At his age of 5 months, I would give a try at gradually introducing some low-allergen solid foods. These would provide alternative carbohydrate sources and reduce the lactose load from the formula. Early solid food introduction is not recommended for breastfed babies as it hurries the transition to the less-protective adult flora, however, a baby receiving any formula has already made this transition, so we don’t have this concern here.
Let me know how it goes and we can come up with other alternative plans, if needed.