If jumping makes your knees hurt, then you have a lack of ability to decelerate. The quantity of jumping the leg matrix is, as you already know, too much for you. So don't do it. You'll need to come up with an alternative that's specifically appropriate to you. The overall principle is that it's a metabolically challenging bodyweight complex. I'd suggest training deceleration, since that's a weakness for you. Some of
Dave Schmitz' lunging band drills would work well in addition to the non-explosive portions of the leg matrix. Look at his Lunges and More PDF file and watch the video from the JP Fitness Summit to see some drills. In the lunges, the band pulls you into the bottom position; that's decelerative training. Especially do the lateral lunging.
I'd also encourage you to include at least one, if not more, corrective mobility drills in your bodyweight complex. They need to be difficult enough to count as metabolically challenging, so something like
spiderman climbs (
video here) would work. Drills from
Magnificent Mobility would work. Some of the drills from this
Continuous Dynamic Warm-up might work.
You decide what you need, what will be tough enough but not injurious. You choose movements that will make you better, not worse. If, after you've put something together, you'd like me to comment on it, I'd be happy to do that.