So this week I found out I have a degenerative arthritic cyst in my knee.
The plan is to control/mitigate it through cortisone and synvisc in injections and "lifestyle" changes.
First, no more running, except for PT tests. Next, dial back on rock bottom squats, which is the only way I do them.
I generally do kettlebell front squats with 2 88lbs kettlebells, super setted with double swings with the same bells.
This morning I attempted to get back to this program, and found a lot of difficulty in stopping at, or just below parallel.
My current plan is to drop down to smaller bells, and retrain my form. Has anyone else dealt with this? Does my plan seem to make sense, or do any of y'all have another idea? 
Would box squats help?
Yep, I'm with Leigh on this one. There was a study recently about patellofemoral stresses at various squat depths and not surprisingly, the lowest forces were above parallel.
Since you're doing a front squat, the hips are farthest from your center of gravity at about parallel, which might help explain the difficulty of reversing there, besides the fact that you're not used to it.
Thanks guys.
I guess I'll try half squats. Box squats would accomplish this same patellofemoral stress as stopping and reversing direction.
My ego might not be able to handle that though!
Haha we do what we must to stay strong homie. It won't be that bad.