I've looked at the Motul website recently and remember the 5w40 oil being API SL and the 10w40 being API SG. This means that the 10w40 will have more zinc and phosphorus...and that's a good think in that rocket ship you bought. Further the 10w40 should have less, or no, viscosity index improvers, meaning it will shear less. My vote is for the 10w40.
As far as filters go, I currently own 6 quads and race 4 of them and have used every brand of filter out there; can't tell a difference, except in the wallet. If it were me, I'd go to ebay and look for Hiflo in a six pack and keep them changed pretty regular along with the oil. Just because it's expensive, fancy, ester oil doesn't mean it's gonna last forever in your new X. I'd say 10 hours max, half that if you're racing it.
Enjoy your new ride, should be fun in your neck of the woods, I've seen some great riding up there in Pa. A good friend of mine down here moved from somewhere in Pa, he tells great stories about riding in coal country. Anyway, be safe and get your BRAAAAAAAAP on!