Sorry for the delay here. With 3 hours of PT a day, 2200 cals / 40g of protein is certainly going to be a major factor in his lack of recovery. If you could get that even to 2800/150, that would be much better, albeit still definitely too low but I don't know how realistic 3500/200 is.
I'm trying to figure out what happened here though. Going up in 5 lb increments on the bench for 7 months, 6 times a month should have yielded a ~250x5 bench. The guy weighs less than 200. Did he not practice pushups AT ALL before his APFT?!