What on earth are you doing in the gym every day? If you're using a gym for strength gains, then one hour two days a week is more than enough for most traceurs- especially since it's just a means to an end i.e. there's no point spending all that time getting stronger if you're not gonna apply it to movement. Strength training at the gym for a traceur every day is a complete waste of time. Your body does not get strong when you train, it gets strong when you rest. If you lift (heavy) in the gym for an hour, twice a week, as a supplement to your other types of training you'll see more gains faster.
As for your aches, the cause could be a number of things. Lack of flexibility, muscular imbalance, overtraining, impaired muscular activation. Without performing a number of tests it's impossible to tell what's causing the pain. The only thing I can recommend is the same as Dave.... rest. If you still have problems after a good rest followed by light training then you'll at least have eliminated overtraining from the cause and it's time to look to other potential causes.
See this as your first real test of parkour- you have a problem you must overcome. Eliminate each potential cause one by one until you find out what the real cause of the pain is. You'll learn quite a bit about yourself, your limits, abilites and strengths as you do. Good luck