I'm guessing what you mean is that the engine didn't have this "click" before you took out the piston and liner. The first thing that's come to mind is to wonder if you put the piston and rod back the same way it came out. The rod only fits one way because there's a tiny chamfer inside one end of the bush and this chamfer has to face the crankshaft to give a clearance for the radius ground on the crankpin. If the rod's in the wrong way then the piston will also be in the wrong way round for the way it's been run in. This may be giving some extra pinch causing the click which is just the clearance in the rod bushes changing from one side to the other.