if your engine is in bits then nothing works better than hot soapy water. seriously. soapy water all over the bores etc, high pressure wash your gallerys and make sure it is BONE DRY before you do anything else to it.
its worth going out and finding a pack of white rags too to wipe it down. you use white so you can see if there is any grey matter left on your parts. if there is grey, then wash it again.
the carbon on pistons is a bitch. if your not watching your CR too closely use a wire wheel on a drill. otherwise just leave it. some people say that carbon build-up on pistons and cylinder heads can actually be good for your engines performance.