When I was having rehab after a bad accident, the Physiotherapist who was doing the rehab sent me to another once my muscles had strengthened enough. The new Physiotherapist was/is also a practicing, qualified Pilates Instructor. We did Mat Pilates only. As you have trouble with your joints, I strongly suggest that you get a referral to a Physiotherapist who also practices Pilates, so that you can be given the appropriate exercises for you, and steered away for the more harmful ones - and believe me, there WILL be harmful ones, but they will have to assess you first.
The first Physiotherapist got me using a gym ball and initially I just did 5 minutes gentle warm-ups in the morning and again in the afternoon. After a week or so, she built on that slightly with the length of time, and a couple more exercises. It was only after my back and deep abdominals were strengthened enough that I went on to the more formal Mat Pilates.
Another thing that MIGHT be beneficial is hydrotherapy. Walking in a pool is excellent - if you are in the northern hemisphere it might need to be a heated pool!
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