It has 100k miles and the previous owner rebuilt the engine with racing pistons & valves (carrillo CP). overall car looks decent shapes but I wonder if this engine sound is normal at idling.

 

From that video, sounds normal…

 

Is the knocking noise normal? is it just from the vacuum pump or something?

 

The sound of the engine looks normal, the knocking sound looks like release bearing from clutch (should stop when you press the pedal clutch).

 

that's actually automatic transmission.

 

I'm late to this - but agree on it could be the vacuum pump. I just replaced mine:

https://www.ecstuning.com/b-pierburg...667556919~pie/

 

I had some weird noises on my clubman. Replaced the friction wheel, but the real issue was an aftermarket (continental) belt. I replaced with a dayco and the sound went away. It's a noisy motor even when it's running right.