On average, 30-45 minutes is quite reasonable for Junior High age kids. Remember that kids generally have a good deal of energy, provided that they are basically healthy. Limits for everyone should be about 70-80 miles a week. More miles run will not equal faster times. If you want to run fast, you do it by practicing running fast, interval workouts.
Individuals vary on how much stress their joints can take without injury.
While there will be occasional aches and pains that are normal for high levels of exercise, kids should not be encouraged to run through severe or chronic pains in the legs. Proper form while running does much to prevent these injuries. A regimen of rest, ice, and ibuprofen are the fastest way to heal minor injuries and get back to full speed. Continued running after an untreated minor injury can lead to chronic injuries. Pool workouts or other non-weight bearing exercise are good substitutes for running during recovery from many minor injuries.