Check engine is flashing, cylinder 3 and 1?

Yes, the intake runner control can cause misfire codes, I would check the valve and its operation, here is the location so you can check it out. Also, I would replace the spark plugs and service the throttle body. Check out the images (below). Please let us know what happens.

I thought number 5 is the runner or are you talking about the electrical part that controls it? How do I check it? remove it and see if it moves when I cycle the engine?

Yes, that is a good way to see if it works. Let me know what happens.

Runners work fine. Do you think this carbon build up is the reason? Not seeing the electrical part that controls the flaps, unless it is the one that has a vacuum line to it, but no way to test it.

Also, i have seen a video that shows that when 3 valves are closed one cylinder valve is open, is that true?

Thanks for the videos. Yes, that is okay that one cylinder has its valve open. It looks like the flapper intake valve is working but about the actuator, does that seem to move at all? It looks like a normal build up, but I would clean the flapper valve and intake runners.

What is the flapper valve? Am only moving the rounded black piece which has an arm.

Yes the part inside the intake looks like it is working I was asking about the actuator part.

What actuator part, how do i check it?

It would be the part that attaches to the flapper arm. See if it moves when you turn the key on?

I bought a new intake which comes with the new arm valve as it has lots of carbon inside it, and this new one has the updated version which does not break easily.

Good to know, please get back to us on what happens.