I agree with Aly. I too have knee and hip pain at times. The best thing for me was eliminating jogging/running. It makes me very frustrated to do this, but in the long run it will save my knees and hips.
Also, give your body time to work up to what your mind can handle. Our minds can go a mile a minute, but our body's are screaming, "NO!!!" Listen to your body. This again, is something I had to do.
I was having soreness in my knees, hips and my ankle (I strained it earlier in the summer and didn't realize it wasn't completely healed). Anyway, I took my exercise down a couple notches. I had been doing some heavy circuit training that my mind could handle, but my body couldn't LOL. I've cut that out for a few weeks.
My schedule had been: circuit train 2-3 days a week, 30 day shred 2 days a week and biking 3-4 days a week. It was a bit too much.
So, I cut down. For about a week almost 2, I only went cycling. No circuit and no 30DS. I did also some arm exercises and aerobics to help a bit. I did start a strength training program. 100pushups, 200 situps and 200 squats (which would help majorly strengthen your body) as well. That is 3 days each week.
This week I added in 30 day shred. However, I only do it 2 days a week right now.
I will continue at this level for 1-2 more weeks, then I will add in a day of circuit training.
This was incredibly frustrating and challenging to do, but I feel like I've given my body the time it needed to heal up and recoup.
It is recommended too to take a "rest" week every 6-8 weeks. That may not be a bad idea. This gives your body a chance to recoup.
Also, make sure you have good footwear. This makes a WORLD of difference on your joints!!
I hope this helps a bit. I know it will be challenging, but you will be better off if you cut a couple things out and regroup a little bit. Then over the span of a month or 2, add more things on, but slowly.