Knee template- swelling week 4

Posting here as it seems the knee template sticky is dead. If not please delete.

Hi, I have had pain, swelling, weakness etc, in both knees, on and off, for the past 3 years.
It started with my left knee, but it’s my right knee that is giving me the most problems now.
I had an MRI done in April last year. The analysis by the doctor wasn’t very helpful – essentially, now that I’m 42, just limit my exercise and ROM, no running etc.
I do see from the notes, under ‘impressions’ that it lists (for both knees):

  1. Remote injury of the superficial medial collateral and lateral collateral ligaments.
  2. Popliteus Tendinosis
  3. Mild intrasubstance degeneration for both menisci. Anyway, once the swelling had gone down, I was able to squat regularly using the SS NLP. All ok, until about 3 months ago, when it reoccurred – I have no idea what triggered it. I went to squat (I noticed it wasn’t 100% before, but continued), and then my right knee just gave way after about 2 reps.

I wanted to sort this out properly. Hence, I bought the Knee Rehab template.

On Week 4, Day 2, I did 3-2-0 tempo squats and single leg bird squats. All at the prescribed sets and reps etc. The tempo squats felt good – the first time I had been able to squat without the aid of pins or a box in over three months. The single leg bird squats were a challenge, but I got through them. Since then, my right knee has become slightly swollen, is tight when I bend it, and I have some mild discomfort. I had no issues when I did conventional deadlifts on Day 3, although I decided to only do one set of Bulgarian split squats (no weight) so not to aggravate my right knee.

Since I started the template, I feel that my knees and quads have strengthened – I think this is probably due to the isometrics (Spanish Squats, Isometric Squat and Wall Sits).
I think the single leg bird squats were too much. I have low bar squat programmed for Week 5, Day 1, and I really hope I’ll be able to do that without issue.
How should I proceed? Continue with the exercises in the program with no change? Add back in isometrics (a killer, but effective)?

Any advice would be much appreciated.
​​