Just got back from checking the whole work I did. I would have to pull out the intake manifold.
Then I was thinking. The sound is caused by moving parts, so, it should be the engine or the serpentine belt and timing belt zone.

When I had started the car, the sound did not sound like knocking sound; it was not heavy.
It sounded kinda "practa practa practa practa practa . . . " in quick succession.
It sounded like there is a free-willing nut or metal object inside something some moving heavy metals.
I was thinking, maybe some nut may have falling into the engine block, but where.
In my work, the opening to the engine were through the spark plugs, when the oil pan was pulled or the opening through the breather box.
Or could it be the VVT?

The interesting is, manually turning the engine does not produce any noise. I turned it hand full of times, no noise. One thing I experiences was, manually cranking the engine, the turn does not go smoothly. Every about (clock term) 25mins, the turn would hold a little, that is, I would have to put force to it to turn; not much force but significant enough to bring it up here. If the breaker bar is at 12oclock, it hold up at 12:25 (clock time). At 11:45, the bar held up (tighter) at 12:10, and so on.

I am really not in the best of mood about my issue here, after all the work I've done. Oh well, such is life.

Hope you all had good enough Thanksgiving period.