Are you running somewhere with an incline so at some point your running down hill? How old are your running shoes? They should be no more than six months old as at about 6 months they break down, this is ESSENTIAL if you're going to be jogging.
Are you icing them now? Do that for sure and take an antiinflammatory.
I have a bad back, and I can't do anything that is high impact [most running, power skipping, jumping, etc] so it was really important that when I started running I did so with the proper form, and it helped me avoid knee pain. When you're running be sure not to throw your feet down onto the ground, gently place them down, even if it means slowing down your jog a bit -- once you're body gets used to the impact and you improve you'll be able to pick up the pace.
Also, you may want to consider doing some thigh strengthening exercises along with the program you're doing.
[I also have a torn meniscuis, which is in your knee so I have to be very careful not to hurt my knee while jogging which I probably shouldn't do anyway and these are the things I've done to keep it in check, I hope they help you!]
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