Using a JR Pass? - You could ask the agent to look for a pair of D&E seats between Nagoya and Tokyo. If that can be done, then you can ask if there are two other seats in the same car between Kyoto and Nagoya (perhaps B&C seats). You will need to do a shuffle at Nagoya - but most of your trip is spent in the seats you want.

Not using a JR Pass? - Consider paying the supplement for the green car.

There is no online service to do this in English.

BTW - Avoid car 4 (I think). Car 4 used to be used for smoking cars, but it is now a non smoking car. The same rolling stock is in the same position in the train... so it stinks of stale cigarettes but you're not allowed to light one up.