i dont think emancipation007 means to clean his engine...
after rebuilding a engine it should work the same as what it did from new it also depends on how much you rebuild and for what reason you are rebuilding it...
replacing bearings and rods wont change the perfomance unless you replace them with ones that were not standard and also if you dont check them regularly and let them affect your tune...
you may have to run your motor in again if you do a full rebuild but if replacing bearings and rods i just like to run the car rich and just take it easy for 2 tanks or so...
you also need to look at wether its goin to be worth rebuilding cause depending on your motor it might be cheaper to just replace it..