Alright, pictures are good. Posting them really helps. I don't see anything bad happening in that picture, although I can't see the entire inside of the cylinder, if there is a large vertical gouge that would be a problem but I don't see that. It don't look like a problem. If you don't see anything bad on the piston the top end should be ok. I think you can put that back together. Don't forget to line the rings up with the pins and squeeze the rings together to get the cylinder back on, you don't want to break the rings putting it back on. Also, make sure the base gasket is good before you put the cylinder on.
However, when you release the clutch lever (and engage the motor) the compression should happen instantaneously, it shouldn't take 3 seconds! Are you sure the clutch is working right? When you pull in the clutch lever the back wheel should spin freely and the instant you release it it should immediately be more difficult to move because of the compression. If this is not happening you probably just need to adjust the clutch cable or clutch itself.
Also, tell me more about this "debris" you found? How much was there? Where was it? Was it particles of rubber? You should remove the magno case plate and check the rubber seals!