I went through the same thing over a year ago when I first got on to the department.
Our training academy was all about running, stretching and calisthenics. We did tons of pushups, situps, leg raises and crunches. When I first started I could do 60 plus good quality pushups in a row. After I graduated and was sworn (not lifting during the academy) I struggled to hit 50 in a row. Sounds crazy but it happened. I'm not that big (180lbs at 5'8" with a bf% of 10-12 now).
During the academy, I dropped down to 168ish and bf% went UP to roughly 15%! It was the poor eating habits and lack of weight training. They stress the shit out of you and you have a very hard time sticking to a good plan.
I'd suggest having all your food prepared every day, buy a bunch of bars (we would get very short breaks and I needed something fast and convenient) and take in as much lean protein as you can. Your diet should be a bodybuilders diet and as clean as possible. Try and lift on both weekend days and stick to the big compound movements. If I could start over I'd do just that. Instead, I'd start my day with an MRP and go downhill after that.
My physique looks good now but like shit when I finished the academy. Took me a solid 3 months to get back to where I was before.
Oh, a ton of my fellow officers bodybuild, we have some monstrous guys working in Chicago/Cook County. Lots are juicin and they don't test for that.