The thread below is related to this:
Apparently the 2nd edition e-book for 5/3/1 has templates that incorporate crossfit style programming with the 5/3/1 program. I have the 1st edition and Wendler addresses using bodyweight assistance with the big lifts in it so I am sure he does this as well in the 2nd.
Anyway, this would allow you to progress in the bench, squat, military press, and deadlift while upping your conditioning to meet your goals.
Just something to consider.