Bennie, I'm ""ASSUMING"" you are hearing the powervalves rattle. It is pretty normal, if you hit the throttle at idle, will it go away? If so, it is more than likely the powervalves. The KDX's were horrible for this. The transmission noise I'm betting is you hearing the chain running or the clutch spinning. CHange your oil soon too. I usally change the oil right after a break in. Everybody has their oppinions on breaking in their bikes. I usally idle it until warm, let it cool completely, ride it the next day until hot, let it cool, then run it and that is it. Never locked a motor due to imporper warmup. Just by losing waterpumps and crushing rod bearings that were long over due (10 years on a cr125 rod bearing, lots of abuse).
Use the search function and look for breakins if you want to learn more. Lots of good information on the KX in general is here.
Green is a great machine! I love the KX500, and now my KX250 has become my love. But, I will be honest and say that the YZ250 spanks the KX anyday on the track. Owning both, I can say that without a doubt. But, the KX is a sweet ride, I would not have purchased it if that was the case.