ALH Rolling Black Smoke and Surging

2003 VW Jetta 1.9L TDI ALH Auto trans
Bought Jetta with a blown engine. Bought an engine from the junk yard that was running. It came out of an 00'-01' Beetle. Completely went through the engine and checked it all out. I used the injectors out of the original engine but the injection pump is out of the beetle engine. They are both 11mm pumps. I started the motor today for the first time and it starts fine, runs about 3-5 seconds then starts surging and bellowing black smoke. When you push the accelerator pedal nothing really happens. I started it several times and after the engine warmed up a bit it smoothed out and gradually quit smoking. I let the engine idle for about an hour and would occasionally mash the accelerator down to about 3500 rpms. It was a bit sluggish but would accelerate with no problem. I let the motor cool off and restarted the engine and now the same symptoms are occurring again.
Looking for input and advice. Thanks.
I have searched the forums and haven't found anything that's exactly like the symptoms I am having.

If the turbo went on the Jetta then it's likely that it sent slugs of oil into the intercooler. Oil will also end up in the exhaust, in which case it might be a while before that gets burned out.

I would be careful until you're confident that you're not going to blow this engine. Because it's mostly an unknown I'd do a compression test on it. If compression is good then you should be good to start "polishing" things.

Where did the new engine come from? How long was it setting? Might be that it's in need of blowing out some cobwebs (but first do the above). Maybe doing a Diesel Purge would be of benefit. Check vacuum lines. Check timing (note comment about TB below).

You really have a lot of unknowns here. Need to start out from scratch and establish some sound baselines. Unless you know that the TB was changed in the new engine (are very sure) you're going to want to change it (and all associated/typical parts).

New Timing Belt, New Turbo, Reworked Head. It has a straight pipe (not my idea, previous owner). Like I said I COMPLETELY went through the engine. The only old parts on the engine are the block, crank, rods, injection pump and injectors from the Jetta (that I know were fine before the engine blew) (also the head but it was reworked). Not new to diesels as some may think by reading my post...been making a living working on them for twenty years now. That being said this is my first time owning a VW. I have done numerous timing belt jobs in the past and haven't had any problems. I own the metalnerd tools to do the job. Also completely removed entire CAC system and cleaned.

I didn't see in your response that you'd checked the intercooler.

IQ might be set too low.

What's the ambient air temperature? Might be a bad CTS.

And... what about the MAF?

Do you have VCDS?

Can't check IQ until I get VAG COM

Unfortunately I don't have VCDS, I am going to call Ross-Tech first thing in the morning and order it. My current OBDII diagnostic tool doesn't support everything.

Ambient air temp is about 45 to 50 degrees.

Can't remember MAF off the top of my head, but I will check it in the morning when I get back to the shop.

I wonder if it might possibly be the N108 Valve in the injection pump. I don't know how long the engine sat at the junkyard. Hummm...any thoughts?

All kinds of possible contributors. At this point best to sit tight and wait for VCDS to show up.

Running a Diesel Purge wouldn't be a bad idea. How many miles on the IP and injectors?

Might try just unplugging the MAF and see if that makes a difference (expect it to be sluggish, but smooth if it's a MAF issue).

Also, I find that my cars are less than stellar at starting when temps are cool but not yet at the GP threshold. Doubt that this is the source of your woes here, but it might be just a little more salt in the wounds. A bad CTS (Coolant Temperature Sensor) can also compound things: if it's black then, yes, replace it (replacements are newer rev'd and are green).

OK, after doing a ton of research and checking this and checking that I finally read a thread with a similar symptom. I believe my problem might be related to the N18 valve.

You see now my engine would only start and run for a few seconds and then die. Every now and then I could get it running for longer and when it did run for a longer period of time, it would roll the black smoke and had a really rough idle.

So after doing some reading and digging through the threads I found a post about the N18 valve. I went out to the shop and unplugged the vacuum line going to my EGR valve and viola problem gone. It starts and runs fine and when I place the vacuum line back on the EGR valve the symptoms would come back and literally kill the engine.

Now all I have to do is diagnose the cause of this and find a fix. VCDS will be here tomorrow so that will be a tremendous help!

Anyone know the proper way to diagnose the root of this concern? I'm leaning towards a faulty N18 valve.

Subscribed to this thread. Looking forward to hearing what you find!

You could swap the N18 and N75 around: usually the swap is to verify the integrity of the N75, but in this case it could work the other way around; however, I'd only look to do this for checking idle conditions (anything else and you're likely going to get improper response -due to a bad N18- from your turbo).

Sounds like bad pump timing to me.