well my first guess is your squatting too often. I know I could no way progress with doing them 3 times a week, not even twice a week.
After almost half a year I would say yeah you could try the madcow variation. It still has you squatting 3 times a week but the medium squat day bridges the gap between adding 5lbs to your 5 rep sets, same for both bench and rows aswell as squats. Deads and military are only once a week instead of three times every 14 days like your doing now.
In all it should allow you to recovery more between workouts. The assistance lifts are situps, hypers, dips, curls, tri extensions. Iv heard of people adding in chinups/pullups too...