You are probably trying to do too much too fast. Your joints and bones just aren't ready for it yet. Try to do some weight training as well. Standing calf raises not only build up the calves but strengthen the ankles. Leg extensions and squats are good for the knees - BUT YOU HAVE TO BE CAREFUL NOT TO LIFT TOO HEAVY.
As for the jogging, I recommend you read Running Until You're 100 by Jeff Galloway. It shows you how to ease into it. I'm doing it right now and love the way my body is responding. I walk for two blocks and then run one block, right now. When I first stared I walked for a minute and ran for just a few seconds. The running is slow and easy - not a race.
Easing into it will help your body to get used to things and not get injured - causing setbacks.
Good luck and have fun!!!!!!
To save strain on your knees and ankles: You need to build up your quads. The support the bulk of the weight and divert the most impact.
Squats are good for the quads.
Ride your bike! ^^
Ankles are easy. If you wanna do just the ankles, sit down & put a barbell across your feet. Tilt them back and just move em up and down in unison. Will probably feel it a little in your calf muscles too.
Or you could do toe raises. Same principle but without the bar across your feet. Can hold a bar or dumbbells for more resistance.
Knees? Best thing I found was leg extensions. That builds up the muscles around the knee, and the thigh/calf muscles for better support of the knee.
It's high impact on both your knees and ankles. Make sure you have the absolute right pair of shoes with a high level of support, and I suggest sticking to light walking, a cross trainer or a bike for the first few months, then easing into jogging and running when you have strengthened your muscles. It's not worth hurting yourself and taking three steps back every other month, especially when there are other suitable alternatives.
Good luck, let us know how it goes :)