Nah, that's bullshit. As long as the modifications that you did, didn't cause the problem in any forseable way, then they can't deny you warranty work, just on the basis that it's modified. For example, if your car is leaking oil due to a leaky gasket, they can't blame that on your mods, as they in no way could possibly affect your gaskets. But, if you have a problem with say your throttle body, then they can say that you modified the intake, and that's why the throttle body failed. Bottom line, if they really want to, they can find a way to screw with you. If it's something you think is major, then put all your factory stuff back on just for the trip. If not, I wouldn't worry about it.

Have you tried getting balanced yet....that sounds like it could be your problem. You may want to try that first, it's a cheap sollution to a problem that might just be regular maintenence.

Later,
Aj