Having strung and measured both the N and K90's, I can tell you they are both the exact same size.
The reason that Fed has more trouble on clay vs. other surfaces is that Fed likes to take the ball early, and with a true bouncing surface his timing is perfect and he makes it look easy.
On clay however, the bounce is not true bouncing most of the time, especially when the clay gets rippled from a lot of ball bounces. This can make the ball take crazy bounces, which will put a lot of pressure on anyone trying to take the ball early.
This is why so many clay courters like Nadal, Moya, Ferrer, etc., stand so far back to give them time to line up their shots. That is not Fed's natural game which will always make it harder for Fed to win the French.