Yes, the plugs and oil intervals can be reset whenever you want to (Yorgi has a great DYI in the 6er DIY section). But I would not think that is the case.
Personaly I would change the tranny fluid. I'm sure you will hear many opinions, but that is mine. The rough shifting is normal. The car is down shifting to help you turn or slow down. As you get used to the way the car drives it will just get smoother.
One other thing you should do is reset the transmission. Turn the ignition on (engine off) and hold the gas peddle to the floor for 60 seconds. That will reset the tranny and it will start to learn your style of driving.
'07 650i Coupe - Black Sapphire Metallic
M6 bumpers, skirts & wheels
BMW M Cross Spoke Composite 101 Rims 20"
HUD, Comfort Access