I hear what you are saying. I too have wondered if it could be in the transmission but why would it be quieter with the new motor and at first nonexistent after the swap? I have put a stethoscope on every part that I can think of and really cant hear it coming from any part but you take the scope off and you hear it.
I also had about 6 other people with automotive background listen with the scope with no luck ether. the weird part is on the old motor it never went away, on the new one it does and it's the exact same sound.
it make me think it's maybe a piston clearance issue. it seems to sometimes go away when I run it a Little harder like the piston expanded from the heat taking up some of the slop and maybe the old motor was so worn that even with it expanding it wasn't enough. this is just my theory I know some one will tell me I'm on crack but I've had two Chevy's that have rattled like a diesel until they warmed up.
also will wrist pin noise sound like a Knock at idle?