I use brakecleaner and a clean toothbrush. Just make sure you remove all the rubber o-rings from the engine or the brakecleaner might damage them. Also remove the outer seal(s) from the front bearing so you can get it clean too. Spray the cleaner and rub it clean
A nice little trick to clean and polish the combustion chamber is to rub it with a wooden stick, for an example a match.
Lube everything with motor oil while putting the engine together. Make sure all the metal parts have oil coat on them or they might rust (moisture from air).