Painful Joints.

Backstory
-Weight has yo-yo'd my entire life, and am at the moment morbidly obese.
-Had multiple injuries in my childhood (we owned a trampoline)
-Was diagnosed with an MCL tear in high school. However, I had it (left knee) exray'd last year and was told it was an ACL tear.
-My left knee cap is offset
-I have bone islands and bone spurs in my knee and ankle joints
-I've rolled my left ankle so many times, it is permanently unstable. As the doctor said, the ligaments in my ankle are like "the waistband from an old pair of underwear."
-I now have osteoarthritis in both knees

I made this list to give you perspective. I work out 5 days a week. Mondays & Wednesdays I use the Precor CrossTrainer (I think that is what its called) for 45 minutes. Its like an elliptical, but on rollers.
Tuesdays, Thursdays, and Fridays, I attend a class at work. Its basically ciruit-training. We do presses, rows, squats, stupups, pushups, planks, lunges, etc. We also use a stability ball, as well as that half stability ball.
One would think all of this exercise would be helping my joints feel better, however, the pain is worse. Much worse. It is especially bad when we to lunges. Sometimes I have a difficult time walking without holding onto something for support after these workouts.
Discontinuing my workouts aren't an option for me, however, I was hoping some of you have suggestions to help alleviate some of his joint pain, or at least modifications to step ups and lunges. I'm also terrified of standing on that half-stability ball for fear of re-spraining something and making the problem worse. Any reasonable suggestions are appreciated!