When you engage the starter-engine and when you cut the motor-engine, the mechanisme makes quite a knocking, metallic noise. That's normal and is caused by the way the mechanism that (dis)connects the starterengine with the engine works.
If thats is what you are talking about then I think there is no problem.
I'm running in my overhauled 3AJ and, when the engine is real hot, notice one loud metallic 'clang'-noise at the moment the engine takes over de starterengine. This is one single 'clang', louder then the ussual starting noise. I'm not sure yet what causes this, but may be anybody has suggestions/experiences with this?