is head gasket size ok , very important so piston won't contact cylinder head?

This is good, everything you find that is good is one step closer to the solution.

Height the same is good, but if there is any spring pressure at all they'll all be closed unless the valve/seat is damaged, and I assumed you checked for all that before you put the head on.
What you need to do is to try to press down on each stem and see how much pressure you need to depress it.
What you are looking for is one that is too easy to push down. If you have a valve spring tool, you can use that to anchor the end of your pry bar and get some leverage on it. Should be hard to depress.

I'd also take the time to mike the camshaft lobes. The book has the spec. I'd be looking for some significant flat spots.

WRT wrist pins, or rod bearings for that matter, it does not take much play to be problematic. IIRc the spec is for just a few thousands play, like 2 or 3? It has been a couple of years since I looked at that, but it is not much. So what you are looking for is a fairly small amount of play in the piston travel. Any perceptible movement is too much. I'd stick a long smooth rod, like an 18" 1/4 drive extension down the injector hole, (after I was sure the hole was CLEAN), and have a helper rotate the engine while I watched the rod go up, hit TDC and then start back down. once it starts down, JUST after TDC, then I would push on the rod with a pry bar and feel for any movement at all. I would check all 4 cylinders.

If none of those pan out then I would start looking at the lube oil channels in the head and make sure that you have no blockages there. A sticky lifter could do this too, maybe. I'm hoping that you saved the old rockers and marked where each came from?

After that, I'm out of ideas.

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very good idea LMW. bad lifter or plugged oil gallery can do this.

I have the old rockers, and no, I didn't mark where they came from. I generally only worry about broken rockers, and there were 2 broken lifters but no broken rockers. None of the rockers looked like they had collapsed either, so I'm fairly sure the cams are fine. I have to stop for the time being b/c I have to drive back to Florida for a few days.

Now I'm off to dinner, be back later with more observations.

Ok, the exhaustion is passing a little... Thinking about the head gasket question. I honestly don't know if this is the factory gasket for this engine or if someone had pulled the head and messed with it, BUT - If the gasket was wrong, wouldn't that lead to the pistons jam-stopping against the bottom of the head instantly and not rotating at all? When the head was off, I looked at it and didn't see anything out of the ordinary. Valves all looked good and closed.

I did manage to forget to clean the bottom of the injector bores as well as I usually do, I had taken the head to a car wash and power washed it and the valve cover, but I forgot to do the seats with the shotgun cleaning mop.

The next time I will be able to work on this is probably Wednesday, I can drive back up on Tuesday.

I wonder why you're getting the code for injector... If you swap that injector with another one, does the code "move" to the other cylinder?

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No - It stays with Cylinder #3. The code is a misfire code, that is just because the computer can "see" the crank or camshaft speed wobbling or senses it somewhere else along the line. It knows something isn't proper, and has calculated it back to the #3... But that doesn't mean that it IS in the #3. My first CRD when the second engine failed, that was coding for a misfire in #3, but it was the #4 rod that fell apart and punched out the wall of the block.

Going strictly by the appearance of the pistons, I'm thinking if any are the problem here, it will be #2. The pistons all were dry looking, except the #2 was wet and greasy on top. It could have been from the coolant dribbling when I removed the head, or it could have been something more. When I get back to Savannah, the next step is to pull the head again (I hate doing that) and take it to a head shop for a thorough cleaning and check. If that comes back inconclusive... Then I have to look at pulling the block.

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Bad noises = REALLY bad things.

Patience, Geordi. Beware of speculating too far in advance of the data. Before you jump to any conclusions, I'd do the checks I suggested above, which do not require that the head be removed. Make *sure* that the springs are good, that valves don't stick, and make sure that the camshafts and the cam bearings are good. If the cams are good, and the rockers etc are good, then you pull the head and check it more thoroughly. If the head checks out, then it has to be a block problem either a wrist pin or a rod bearing. Severe rod or wristpin wear you can sometimes find if you have a large adjustable wrench that can be firmly tightened down on the crankbolt; sometimes rocking that back and forth will let you feel the clunk of a bad bearing.

Good luck! I have no doubt that you will succeed where the stealerships failed. Call if I can help.
best regards, LMW

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yes , start looking into , cylinder misfire ? comp test , oil press manual gauge test , metal in oil .?

As I state in an earlier post this needs to be done as it will tell you where to start looking for your problems. If you have low pressure idling and it comes up when increasing the RPM but not with in the normal range then you know you have to pull the engine.

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I'm not that worried about the oil pressure, the idiot light is finicky enough that there have been plenty of people scared by it lighting up without reason - there has to be sufficient pressure to keep the light off, and a worn sensor gets MORE likely to light up, not less. A broken circuit (unplugged) means the light is on all the time.

The idiot light works - it is on when the engine is stopped, and off when the engine is running. Since the oil pump is a gear pump, it cannot help but be running. Maybe the oil supply is barely sufficient for idle, but the noises get louder above idle, not quieter. This also suggests that the oil is not the cause.

I am on the way back to Savannah right now and might have a chance to poke at it a bit more in the next few days, so hopefully something will present itself when I start checking theories.

oil press is important to a hydraulic lifter ,, if is low or lifter seat in cylinder head is worn out , it can be excessive valve lash ?

Checking the oil pressure with a mechanical gauge has nothing to do with the oil. It will tell you have if have a stacked bearing.

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I'm sorry, I have no understanding what you are saying. How can oil pressure tell me anything about bearings, and how can bearings "stack" and what bearings would be able to do whatever this is?

I am very confused.

Ok. A stacked bearing is a spun bearing. To explain this I'll be using a small bock Chevy as that is what I raced and know the oil pressures without looking anything up. A warmed up engine has a idling pressure of 20-25psi. once the rpm's come up it should be around 2000 up 30-35. These pressures freak most people out who aren't familiar with SB Chevys. A good rule of thumb is a difference of drop 10 psi from operating rpm to idle.

Now I have a engine with a knock and as I rev it up it gets louder. If it is a spun bearing the noise is because you now have a gap between the rod and crank where the bearing was. So with a mechanical gauge not electric you see the idle pressure at 0 to 10 psi and you now rev it up and it comes up say 10 psi maybe 15 you know it is time to pull the engine. This is because with good bearing the clearance is .0015 to .003 your creating resistance and this is what builds pressure. Now the thickness of the bearing is about 0.125. So with a spun bearing you can see the clearance is far greater less resistance lower pressure.

Imagine you take a garden hose with a pressure gauge on it. You will have a base pressure and when you put your thumb over the end to create resistance by blocking of part of the flow you will see the pressure rise. So imagine the pressure with you thumb over it is your operating pressure and when you remove your thumb the pressure drops because you now have less resistance, which would be the 0.125 gap now because half your bearing is gone.

Now your thinking that if I have 0.125 thick bearing on both sides and I spin a bearing would the clearance thickness still be the same even thought the bearing is now on the other side. In order to spin a bearing there as been a failure of some kind that has allowed the surface or the bearing to contact the crank. This can be over time or all at once. What is happening is the crank is grinding down the bearing until it is thin enough to spin it around and on top of the other bearing.

Hope this helps. If not post more question and I'll answer them till you understand. If it is easier PM me your phone or I can give you mine and this might be easier than posting back and fourth.

One more note: do not rev the engine up to say 3000 rpm or you might find out real quick that it is a rod as you will be able to see it stick out the side of the block. Then this will be your reaction

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2013 Audi A3 2.0 TDI Premium Plus
1948 T4 Willis Pickup
1993 C3500 Chevy 6.5 Turbo Diesel
1984 C7500 Chevy Flat Bed 366 gas
1987 R25 Chevy 350 gas

the rattle turning into a squeal makes me think spun main bearing. that's my .02. Sorry for your predicament, I know exactly how frustrated you are. I'm fighting a Cat 3208 that overheated and a Deuce-and-a-half with a mutli-fuel that has decided to spontaneously die at idle at random times for no reason.

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Or to put things more simply. If you have good oil pressure when the engine is cold, and it drops off considerably once it warms up, you likely have a lower end bearing problem. The reason is as the oil warms up it flows more freely through the over-sized gaps (due to extreme bearing wear) and the pump can no longer flow enough oil to keep the pressure up. A lower end knock would get worse as the engine warmed up. I can't speak to the reliability/sensitivity of the CRD oil pressure sensor.

If your oil pressure is low when it is cold then it can either be the pump or the lower end. Or your oil has completely broken down due to age or contaminants. Mechanical fuel pumps driven off of a cam concentric are notorious for leaking fuel into the oil. (International/Ford 7.3l IDI, gasser V8s) Bad rings or injectors could also allow unburnt fuel into your oil. In both those cases you tend to 'make oil', but it's easy to diagnose by simply smelling the oil dipstick for fuel.

If you have an OBDII scanner than can monitor PIDs (like a ScanGauge), you could monitor the actual reported oil pressure there.

Like others have noted with bearings and oil pressure, this sounds like a rod knock.

To quote Jeremy Clarkson it sounds "A little bottom endy"

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to me sounds like lifter not getting oil excessive valve lash ,, must check them 2 bad lifters ,also engine misfires on that cylinder ….

Sam, the sound might well be a bottom end problem, but would that cause the pronounced shaking that you see?

LMW

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Grid power- the one true essential

2005 Liberty CRD- ARP studs, Fumoto, Hayden FC, inline Tstat, ETechno 7v GP, Platinum P1, in-tank lift pump.
1983 Volvo D24T
1981 Volvo D24
Dodge Cummins TD
Case 580B
Mitsubishi MT180 diesel
Kubota BX25 diesel