still checking into 6.9 not running right

I removed the valve covers and valves and rockers seem to be ok. I took a cranking video with pump wire unhooked and engine warm. You can see the intake breathing in and out. Does this confirm head gasket problem?

cranking 6.9 video:

http://vid864.photobucket.com/albums/ab210/mmidlam1/6.9%20intake-not%20running_zpsbtignaso.mp4

edit not working...here is the video:

http://vid864.photobucket.com/albums/ab210/mmidlam1/6.9 intake-not running_zpsbtignaso.mp4

Do a compression test to find out which cylinders may be weak, then s leskdown test, from which you can figure out if it's a ring/piston problem, a gasket problem, or a valve problem.

You probably have a compression problem from the sound of it. A compression test would definitely be in order. Keep in mind that the intake air is not throttled on a diesel, so it should always be pulling IN air. A head gasket blown out between two cylinders could cause that as well as a problem with an intake valve - either not closing, burned, bent, or otherwise compromised. There are other possibilities, but those are the two most likely causes.

Popping or puffing through the intake has to be either the intake valve not sealing or the exhaust valve not opening or barely opening. White smoke is unburned fuel, usually caused by low compression.

This won't diagnose your problem but it might help you suspect which cylinder(s) are unhealthy. On a cold engine unplug glow plugs and measure resistance of the glow plugs ( tip to ground ) you need good glow plugs for this to work but on a cold engine they should read pretty low or at least below 10 ohms. Now start the engine and warm it up. What happens to the glow is the resistance will increase the hotter they get, a weak cylinder will be colder than a healthy one so you should see low resistance on the suspect cylinder. Typical healthy cylinder will be 15-25ohms and weak/dead cylinder will stay low or under 10 ohms.

An infrared temp gun pointed at each exh manifold runner should identify a weak/dead cylinder too.

I'm not good with words and explaining much detail but I did find an informative post that follows what I think your problem might be. Without citing the source the OP did approve on copy/paste, here it is.

Sounds like an intake valve issue to me. What I think is happening is the valve seat sealing surface area is not holding the detonation pressure of the fuel. The good thing is if this condition was totally lost it would not be popping like that.

This condition may be due to:
Sticking valve stem.
Carbon/debris on valve seat, damaged/cracked valve/seat.
Weak/ damaged spring.
Worn keeper or worn/damaged spring washer.
Lifter pumping up?

If you continue to operate the engine, for other than diagnostic purposes, you may damage the head, damage the valve, or the engine.

You can look for the valve by removing the covers and observing or measuring the heights of the intake valve stem/spring up as compared to other intakes or at TDC or the start of the compression stroke (both valves up).

OR

Find the cylinder and valve by loosening the fuel line, while the engine is running, until this condition stops. Verify the cylinder by tightening fuel line to create the noise again.
Remove the cover and inspect the valve's height, spring, cap and retainers.

Sometimes it was a worn or damaged spring, more than that was a split valve cap and worn keepers. If the valve stem is nice and free, no wear on stem or guide- reassemble with replaced parts, including seal. Place piston in up position to perform these tasks.

At times, when the valve was sticking and hard to operate, I have cured this problem by cleaning and lubing the valve stem and guide. You need to remove the valve seal to perform this task-with the piston up to prevent the valve from falling down.

Other times when there was debris on the valve seat, I would spin the valve stem SLOWLY, in a drill, applying GENTLE upward pressure after spraying cleaner and lube down the guide/stem in hope for it reaching the seating surfaces. Most times this worked when the owner caught this condition early, the other times required a valve job or new head.

Reassemble with new seal after lubing stem.

While I do not discount your diagnosis, you are also not seeing the BIG PICTURE.
There is more than one problem that can cause this condition. A flat cam lobe can also cause this. A blown head gasket is even more likely.
Logically speaking, problems with intake valves are rare. Intakes to not see the heat of combustion passing by as exhaust valves do. Intake valves are simply not stressed to the same level as exhaust valves.
Head gasket is another potential cause. If a gasket is blown out between two cylinders, it can cause compression pressure from one of the affected cylinders to exit through the intake of the adjacent cylinder if that cylinder is on its intake stroke.
There are several potential causes to this problem. The most important thing is to do diagnosis and not to get tunnel vision.