Becoming A Single Leg Jumper

right now my problem is my knees and shins. I used to be a 1 footed jumper before I started to do strength training, then became a 2 foot jumper. I never used to have any pain when I jumped off 1 foot, but now after a couple reps my knees feel sore, shins might start hurting... it sucks. From my experience I could stretch further when I jumped off 1 so now with my vertical quite a bit higher than it used to be it would be really helpful. I have been doing 1 legged exercises via the VJB for the past 6 weeks... but at the same time my knees haven't felt that great since I've started so I don't think I am going to see any gains until I finish the program and my knees heal up completely.