When you pulled your cylinder, did you check your rings? A dent in the piston means something got in your cylinder. If you cracked a ring (or rings) you might not be getting the compression you should be.
Another good idea is to get some calipers and measure the cylinder width and your piston width. I got an engine once that had the wrong size piston in it. Was ALOT of rattle noise from the piston slapping around inside the cylinder. Remember that the piston is going to be a bit smaller than you cylinder. I've attached a picture (courtesy of Spooky Tooth) that gives you piston diameters for different cylinders.