There is no difference in the jr. champ and the sr. champ karts, the difference is in the engine (jr. champ Animal uses a black plate restricted engine) and in the minimum weight (can vary, but generally 355 for jr. champ and 410 or 420lbs for sr. champ).
The different kart comes into play with the jr. SPORTSMAN champ class. The jr. sportsman champ has a shorter wheelbase and a lower cage height from the ground to the top of the cage. Generally a track wouldn't let you run a jr. sportsman champ in sr. champ class, and based on our experience with an unusually tall (for his age) and commensurately heavy (we gave away 45 lbs on the 315lb min weight for jr. sportsman champ) driver, I'm not sure you could get a jr. sportsman champ to scale anywhere near what it needs in order to handle adequately at sr. champ weight even in the unlikely event the track would let you run it with the sr. champs.
So if it is a JR. champ, take out the restrictor plate, re-jet the carb and go racing. If it's a JR. SPORTSMAN champ, don't bother. Hope this helps clarify the situation.
Mike