Plyo's shouldn't be worked as over-kill, the beginner plyo's and BW is designed to condition your legs for harder levels of plyo training, but not as a muscular endurance activity, not saying that it won't increase your vertical significantly if done properly.
Make sure that you're doing all the exercises properly and are doing the correct number of repetitions. Pay close attention to the workout schedule so you are well aware of what your are to do on certain days, as to not make mistakes.
Static stretch on your recovery days to help reduce muscle soreness.
Check out this thread i made:
Stretching/recovery Thread (plz Sticky!!!!)
Remember not to sacrifice correct form for reps. Quality over quantity.
Also, eat right, this is an important part of recovery.
I advise you to consume about 1.5grams of protein per KG of body weight daily.
Also, avoid caffeine, soft drinks, juices, fast food and other garbage for your system. Load up on carbs, protein, healthy fats(trans or polyunsaturated) from clean whole foods. Drinking enough water is also essential.
Check out the beginners guide to training by Jcsbuck, its a sticky on the jump training and hoop exercises forum. A must read for all people training.