The clutch shouldn't hinder the piston. It's just there to engage the starter to the motor. When it does turn over is it about the same stiffness as your other bike? The spongy feeling that you are describing sounds to me like a slipping clutch. You may think that with only one thousand miles on the bike, how can it be the clutch? You try laying in bed for twenty years and then running around the block. What often happens to the clutch is that the fiber plates will become glazed and begin to slip, even though they have plenty of wear left. My guess is that you need to replace the fiber clutch plates.

Doug - Olympia - Washington
 I don't know how many CTs I have.