Your progress is VERY visible! Good work!
Are you sure what you felt was joint pain? Or was it DOMS, Delayed Onset Muscle Soreness? This soreness usually starts a day or so after you've worked out, and can last a few days.
I'd recommend you do a program like this --->
Beginning Workout Plan which is bodyweight only, and includes lunges along with the exercises you've already been doing. Do this for about 3 months before you try adding in any weights.
Once you've done the beginning workout for about 3 month, you can try this one --->
Intermediate workout. Start with a weight that you can do the last few repetitions of the last set but it's very hard. You might have to experiment to see what weight to start with; it's always better to start lighter, and if you can do 12 reps for 3 sets, the next time you do it, go a little heavier.
You're already doing more cardio than Scooby recommends in those workouts. Try increasing the intensity--walk for a few minutes, then run for a few minutes, then walk, then run. If you increase the intensity, you can shorten your workout time and still burn the same number of calories. This will help your cardio fitness and also help burn fat faster!
This is advice for EVERYONE when starting out, not just girls!
And of course pay attention to nutrition.
You've made great progress! Keep it up!