Trans problem I think

Ok I have a really bad stumble right before it shifts into 2nd. I think its the trans. I already had to have the trans replaced under warrenty 2 years ago. Its an auti by the way just incase. The funny thing about that was I never got an answer from the dealer what was wrong specificly with the trans and what they replaced. So I dont know if they rebuilt gave me a new one or what. All I know is it took them 3 weeks. Anyway the first time I got it replaced or whatever they did to it my car was completely stock. I'm alittle worried I cant get another trans under warrenty. Seeing as I have no money I cant afford to pay out of pocket. Do you think with and intake header and exhaust that would void the warrenty on the trans? I'd take the chip out before i bought it there oviously.also with the stumle does anyone else think that the trans or can something else be causing it?