Possible Problem With New Cat and Muffler

I put on my new Magnaflow cat, Flowmaster 50, and 2.5" pipe yesterday on my 99'. I've noticed since then that it seems to be acting a little weird. Whenever I get ready to come to a stop my engine seems to want to keep going a little. It feels like it wants to upshift for just a second and then downshift quickly. It seems to want to "hover" a little between 30-40mph. Not sure if that makes any sense but would putting all this on affect my IAC, TPS etc.? The check engine light has not come on at any point...