Sounds like it went away and then came back (vibration). Sounds like you took it apart or someone took it apart? to say "pistons and crank were both out". Don't know what "out" means. Must have been "OUT" OF WARRANTY, because no one but authorized shop should take apart. I would have disconnected trans and clutch and run the engine to see if it vibrated. Anyway you don't say what happened between "it's all fixed" and now. There is a reason the would not "touch it" but it's not because of an "assembly line", dealers make GOOD MONEY fixing warranty's.
Bottom line: you are not asking for advice, you didn't ask a question or to be questioned, just an update, so carry on. Hope it's running good now.