If you're having issues with the motor, waiting until you're confident the problem is solved first is a prudent plan. How long to wait though is really hard to say. I barely had my car in the driveway before I started modding. And, as luck would have it, I ended up having a problem with my oil pressure that was a factory fault. I had already modded the car with long tube headers, a supercharger, tune, cold air intake etc...
Now, at that point, I probably could've still had it fixed under warranty, because nothing I had done had anything to do with the oil pressure. But, after doing a lot of reading, I figured it was a faulty oil pump as many have experienced. I made the decision that I wanted to upgrade to a melling high pressure pump anyways, so I installed the pump myself. After finishing, I nearly had a panic attack because the car STILL didn't make any oil pressure. I was seriously regretting my decisions because now, I've messed with the oil system and surely they will void my warranty.
I finally found the problem (they had bent the oil pick up tube when the car was built), and I was able to fix it but it sure would've been nice to have made gm fix THEIR faulty problem. The good news is, I was able to fix it and it wasn't terribly expensive and was a great learning experience.
Ultimately, the decision is yours and really depends on your comfort level. With the modifications I've made, I now have the dream car I've always wanted and I enjoy the hell out of it. I wouldn't have been happy waiting for years to make the car the way I wanted just because I was worried about the warranty.
Just my $.02
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