There is research that indicates high rep protocol is an excellent regimine for lagging body parts. Done in concert with higher weight lower rep workouts there is validity to this workout.
That said--bodyweight squats should not have floored you like this.
To answer your question about recovery, I like to keep mine active. Walk, bikeride, leg press mixed with ice, epsom salt baths are great. Don't forget the importance of post workout nutrition. This really sets up your next workout. Especially after high intensity workouts, pound down the carbs immediately after and in another meal 1-2 hours later.