My brother has just started to do Crossfit workouts with me.

The problem: 

He has a 1 & 1/12 inch difference in the length of his legs. Left is shorter. The difference is in the femur. So I have had him squatting barefoot. This way his hips remain level during the squat but the problem is that if he goes to full extension when he stands his hips will be tilted and this had led to lower back problems in the past. 

The alternative to this is to have him wear his work boots which have a 1 &1/2 inch build up in the left boot. This lets him have horizontal hips at full extension but during the squat his left thigh will be at a different angle to the right and I presume uneven forces on his hips.

My plan so far has been:

Barefoot during squatting, only fully extend the short leg in order to keep hips straight the whole time.

Lots of single leg work, pistols etc.

Now it’s time for him to Oly Lift. Here lies the problem.

He can either wear the built up left boot which lets him reach full extension safely but catch/pull in a position where his legs are uneven.

or

Go barefoot allowing a safer catch/pull but creating a dangerous extension position.