Put the piston/rod in a plastic sandwich bag (to protect your eyes from flying clips). Using needle nose tweezers to remove the clip. If the piston pin is tight I use a Cork that I've cut a recess in to hold the piston so I can lightly tap out the pin without damaging the piston. Use new clips when you fit the new rod again installing them while the piston/rod is inside the bag.

I wouldn't use an old rod to break in a new piston/sleeve. Run it in as all new the same way you did when the engine was new. Replace the rod at the first 5 litres. Changing a rod is all about fatigue and very little to do with wear. Fatigue becomes an issue before the wear does in my experience in racing engines.