I'm too lazy to retype this so I cut and pasted a response I gave on Thumpertalk concerning this same problem.
"Just so you'll know, I put the GYTR Exhaust, Air Filter, and Jet/Needle Kit on our TTR50 and had the exact same problem as you described. I tried the 12.5 (stock) and a 15 pilot jet, along with the recommended 72.5 and a 70 main jet, and went up and down one groove on the needle clip. After spending three days of non-stop carb tweaking, I was ready to put the stock air filter, main jet and needle back on. That's when I held the stock and GYTR needles side by side and noticed that the clip settings were very different on the two needles. If I wanted the clip position to be the same on the new needle as the stock needle, I would have to put the clip on the fifth groove from the bottom, NOT from the top as the directions said. I tried this setting along with the recommended stock pilot (12.5) and the 72.5 main. It worked great, so I haven't put the 15 pilot jet back in. I probably need to post this info on TT so others won't have to go through the same thing I did, only to find out that the instructions are WRONG."
Try this and see if it helps. Ours has run like a champ ever since.