The biggest single advantage to the Skyliner versus the Express is the reserved seating. You get it on the skyliner and not on the commuter. Your level of comfort will dictate. There is no reason to buy Keisei tickets early. Just plan on buying at the airport train station when you arrive. That way, if C&I takes longer than expected and you don't get to the train until rush hour, you could "upgrade" to the Skyliner to avoid the crush.

I don't think there is really a reason to pay for airport transportation at BOTH ends of your trip unless you expect to be traveling every day. Just plan a few days "in town" for one end of the trip or the other and use the 7 day pass for either the first 7 days or the last 7. Subway/train passes (Tokyo) and subway/bus passes (Kyoto) will get you around town without the need for the JR pass. If you are going to use the Keisei line to get into Tokyo, you probably wouldn't need to activate the JR pass until you are ready to leave Tokyo. YMMV.

JR