That's fairly common how the ortho referred you to the PT and the PT referred you to the ortho. The ortho's job is to fix what's broken (or torn, etc.). The PT's job is to get the patient reasonably close to where the patient was before the trauma.
It's the all important bridge from rehab to strength/conditioning that neither specialize at. And that's not necessarily a bad thing. Each person has his unique skill set.
MaximusB makes an excellent point about 90 degrees. At this angle, the knee is quite vulnerable. In fact, orthos and PTs will often place the patient's knee at that angle to test it.
I'm sure you're aware of the seemingly trivial yet highly important things such as hydration, proper foot wear, warming up.
Do keep your knees warm prior to and during the workout. Those neoprene sleeves help some people but it can also compress the patellae. A better option might be those knee warmers that cyclists use on chilly days. It provides just enough compression and retains body heat. The bottom line is, you need to warm up the synovial fluids and keep them warm through out the session.
SMR/static stretch/mobility drills are important. As long as the static stretch PRE and PERI workout do not exceed 10 seconds and are not performed in an aggressive manner, you will not risk down regulating the muscles (ie reducing strength).
Try starting your leg session with a closed chain posterior chain movement. I don't know if you're aware of the Lombard paradox. Essentially, when coming out of the hole in a squat pattern, the hamstring complex assists the glutes and quadriceps even though they should be acting in an antagonistic manner.
Okay, you're saying. That's a nice bit of trivia but how does it effect me...? Well, most people have trouble engaging the posterior chain, so starting off with exercises that target that area will make you more neurally efficient; so when you do move onto a squat pattern, the posterior chain will be "awake and ready to work." Furthermore, the hamstring complex help to isometrically stabilize the knee which is very important.
So, I recommend starting out your workout with RDLs. Do NOT perform these to the point of exhaustion. We want neurally activate and warm up. If you create too much fatigue, they won't be able to help in the squat.
Now, after the squatting is done, you can try being a little more aggressive on the RDLs. You can also include sitting leg curls. This is one where many will disagree with me. They'll argue that open chain movements have no place, that the pelvis is locked in and you're short circuiting the kinetic chain, etc. All valid arguments.
The way I see it, however, is that you may not be able sufficiently strengthen the biceps femoris short head. This is the ONLY muscle in the hamstring complex that flexes at the knee yet nothing else (the other three muscles - biceps femoris long head, semimembranosus/tendinosus - flex at the knee and extend the hip). If the pivot point in the leg curl machine lines up with your knees, and you perform slow eccentrics (two legs concentric, one leg eccentric slowly and under control) you MAY be able add just enough of proper volume.
Of course, someone will argue that when you squat you should also be able to stimulate the biceps femoris short head via the Lombard Paradox. This certainly is possible. However, I think only those with the highest degree of mind-muscle connection can accomplish this.
Now the squatting part...
Drop the leg press out of your routine. Because the pelvis is locked in, the shearing stress will go to the knees. Sure, you can place the feet high on the platform but I still believe there are better options for someone in your place.
Obviously, for a lifter with reasonably healthy knees who is interested in hypertrophy, the leg press is a viable option. So all you BBs out there, please spare the hate comments.
And I also realize that I may sound self-contradicting in that I think the sitting leg curl is okay but the leg press isn't. Keep in mind the former involves flexion at the knees and the latter involves extension.
I would have someone in your place start off with ball squats. Place a stability ball between the small of your back and a wall. Walk your feet out so that when you're in the hole, the tibia is perpendicular to the floor OR less. The stability ball will allow you to flex at the hips first, sit back, and get an overall feel for how your knees are doing before you attempt more aggressive movements. The initial sets should bottom out ABOVE 90. As you warm up, you can go slightly below 90. Do NOT bounce or otherwise rush the point bewteen the eccentric and concentric. A slow tempo is ideal here as you want to strengthen the connective tissue (which the slow eccentric can do) and you want to gauge whether or not you want to take it further in that particular session (nothing wrong with calling it good if you don't feel right).
It's also not a bad idea to place a mini band above the knees when doing the ball squats. This will (hopefully) teach you not to go into valgus (knees caving inward). Direct work such as clam shells are also recommended.
The next move - IF you honestly feel you are ready is either a box squat or reverse band squat. Both will allow you to sit back back back and have a vertical tibia when in the hole.
The reason I keep harping on the vertical tibia is this reinforces a hip dominant squat. As the OP found out first hand, proper glute activation is critical. Also, the hip dominant squat (tibia vertical) tends to create less shearing stress at the knees which is the LAST thing you need right now.
As you progress, you should be able to integrate the quad-dominant squats (tibia past vertical) as well. However, just as most people should perform pull to push in a 2:1 or 3:1 ratio, I believe most people should perform hip-dominant squats in a similar ratio.
A very well-known trainer who writes for magazines recently came out with an article about how your trainer sucks if he tells you to never let your knees go past vertical in a squat movement. Perhaps the editor chopped out the full article. Regardless, the trainer/writer failed to make the distinction between hip and quad dominant squats and why there should be a certain ratio favored towards the hip.
I mentioned the reverse band squats. If you have access to high quality bands and you are willing to go through the learning curve, I sincerely feel this is a fantastic way to be able sit back (hip dominant pattern), have less load on the knees when in the hole, and learn to accelerate (due the accommodating resistance provided by the bands).
As stated before, now you have the option to be a little more aggressive in posterior chain work. Obviously, do NOT grind out reps. And for YOU - I strongly advise that you do not train to failure. Stop each set with at least one perfect rep left in the bank and stop each exercise with one perfect set left in the bank. Ease into it slowly and let the volume take care of the rest.
That's all I can think of now. If you need any clarification or have any comments, post here and I'll check back after my evening clients.