I don't know what this means. You know what to do in the gym, but want suggestions for a routine. You're basing workouts on 5/3/1 but not doing 5/3/1. So, like, what are you doing?
How often are you doing the rec league stuff? How many practices and/or games each week, and how long are practices?
This Ben Bruno article has some good info for knee pain. He actually has a ton of articles that talk about it since he had knee surgery himself a few years ago.
Dan John's Southwood routine is a solid 3 day a week plan that works great with athletes. Depending in what your practices look like, you could add 15-20 minutes of cardio after lifting or on non-training days to bump up the fat loss.
And, of course, tighten up nutrition. Lots of ways to do that depending on how you're currently eating. But if you're doing sports, I wouldn't drop low carb everyday.