Knee'd help with exercise program

It has been a long time since I have posted any questions. I was working out with a trainer up until December. I absolutely LOVED the feeling of lifting weights...but my knees and hips were in such pain.
I have had 5 knee surgeries from 1986 to 1995 (3 reconstructions and 2 scopes)

From January 2014 to March 2014, I had my left knee drained with two cortisone shots. Decided to have it looked into further and have a MRI done on both of my knees. The cartilage damage I expected (played college basketball, still tried to run) , but I wasn't expecting to hear that my left knee ACL descenigrated.

I got scared. I didnt' want to do anything. So as a result, I have become lethargic, and it is showing.

Now it's time for a change. I need to get back in the saddle. I have tried to pick up with Jillian Michael's BR, or thinking about T25 (but heard that is a lot of jumping and plyo). I really need to lean out more and lower my BF%.

Any suggested programs? should I start biking for cardio? Swimming? still lift 3x's a week?
Low impact but effective???