Pain's not good. On the leg extensions, I'd drop the weight and concentrate on the isometric contraction when the leg is completely straight. Watch or put your hand on the VMO and concentrate on activating it. On the squats again I'd drop the weight. What you want to achieve if possible is muscular exhaustion, i.e. you can't do another rep. The number of reps needed to reach this state is immaterial in terms of increasing muscle activation and growth. When I started using weights in the gym as a supplement to my cycling, I started with 30 reps. I'd do 30 reps on each exercise, no matter what it was. When that felt OK, I added a second circuit of 30. So not 2 sets of 30 at each station, but rather 2 circuits of 30. Then 3 circuits of 30. In all cases, choosing weights which by experience gave me failure like on the 28th rep of the last set while using the same weight for all the sets done for a particular exercise. After about three months of that, I was ready to lower the reps and increase weights. I did that every fall for years. It built killer legs but with a downside of having to spend more time in the gym than fewer reps. Worth it though.

High reps don't increase tendon strength as much as using heavy weights does, but it's a safer entry technique as it allows tendon strength to be built up more slowly with less chance of injury.

On all the bent knee exercises, don't allow the knee to flex beyond an included 120° angle during this rehab. That's 60° from straight. Use a mirror if you can. Focus on contracting the VMO. On leg extensions, a maximum 30° angle is better. That's to reduce inward pressure on the patella. On the closed chain exercises, that'll mean you'll be using a quite a bit of weight. Even though my knees are fine now, I don't break 90° on any bent knee exercise: that's about the knee flexion at the top of the pedal stroke and I'm training to ride, not to be a weight lifter or bodybuilder.

Also don't sell the isometric straight leg lifts short. They work, too. That's the reasoning behind the straight leg high kicks I mentioned in that other thread. They're isometric to knee flexion, but with some added mental kick to aid contraction. Interestingly, isometric contractions are more mental than anything: studies have shown that adding weight to the foot during isometric straight leg lifts does not increase the activation.