JD Nelson,
I had ACL reconstruction on my right knee 4 years ago. I am fully recovered as far as abilities go. I used a stationary bike to pump synovial fluid in and out of the joint as well as quarter kneebends. The static postures were mainly done after acheiving some measure of mobility from the aforementioned. If you use the basic horse stance, and stay around a 1/4-1/3 kneebend depth, you will be activating the front/quads more specifically. The deeper you go, the more the glutes and hamstrings come into play. That is not what you want yet, as you already know from your therapist. The VMO portion of the quad is activated by centering your bodyweight on the ball of the foot more so than the heel of the foot. That little adjustment in centering will accelerate the knees recovery and stablization. After a certain level of strength is attained in horse stance, the "Cat Stance" with the injured leg in the rear, takes the recovery phase training up a couple of notches. I know it looks simplistic, what I described, but I am happy with my recovery. MATT FUREY's hindu squat program is very good at bringing the knees to FULL recovery, but this is done after the therapies are no longer a challenge. I can do 4-500 hindu squats and jumping kicks with no problem now and I consider myself non-athletic. I don't mean to sound corny, but patience pays off. If I can feel great, most anyone can. I will be 44 this year. Play with feeling for the floor with the ball of the foot while in horse stance and see how things go for you. I swear by double dosage Glucosamine/Chondroitin for your/our type of injury. It too accelerated my recovery.
Good luck!
white belt