When the engine was rebuilt, were the motor mounts replaced? The new motor mounts are very stiff and transmit more vibration into the body of the car than I like. I have vibration in my Series 3 at idle, which makes my horns vibrate on their mounting brackets.
As for the slapping noise, I’m not sure. I wonder how the cam chain tensioner was installed? Hopefully the little oil spray tube is installed correctly as well and is operating. If its possible to eliminate the engine vibrating into the body finding the other noise may be easier.