Delayed acceleration goes into limp mode

My 2002 jetta tdi started acting up a while ago. It was going into limp mode. and when looking on this site I found it could be the MAF. So I changed it and it seemed to make a difference. I parked it for winter and just pulled it out for another season and found that it is having that problem once again. I will hit the highway and start accelerating and if I'm lucky, it will start to accelerate quicker so I put the pedal to the floor. It smokes black through all the gears up to highway speed not alot but enough to notice. Or if I'm not so lucky, the car will start to accelerate and start to actually speed up but then give a puff of black smoke and go onto limp mode. It is obvious when it accelerates better. It's almost like it takes till 60kmh to spool up the turbo and actually have power... or go into limp mode. It's probably not what's happening but you can definitely feel the second it goes into limp mode. The engine light is on. I haven't checked it in a while but it's been on before for low boost (and MAF fault before I fixed issue) anyone know what might be happening?

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Manual trans? Intercooler empty of oil puddles? Intake/EGR valve clean?
Vacuum hoses fresh? Original turbo? If so, and if driven old lady-style, the turbo could be really coked up.
There are canonical threads here about troubleshooting limp mode. Lengthy checklists. Start with the easy/cheap stuff.

Searching here can be a pain so just stick tdiclub limp mode into your search engine of choice.
Also, you should scan it again.

Its an automatic transmission. I haven't checked out the intercooler yet and I did remove and clean the egr valve, although it wasn't terribly dirty. As far as I know the turbo is original and I definately dont drive it old lady style. I'll be installing a boost gauge so I can see what is really going on. The vacuum lines look older, they have the cloth type wrap on them.

While you had the EGR valve off, did you have a peek down the intake manifold? How did that look?
You seem to indicate the motor will rev higher than you request "by itself"?
That says "runaway in the making" to me. If there's a puddle in the intercooler, your motor could be taking sips of it and fueling itself on it. The puddle is a sign of failing turbo.

In 17 years, the car deserves new vacuum lines IMO, but for me, priority 1 would be check for oil in the intercooler.
Also, black smoke is unburnt fuel. You could have multiple issues cropping up at once. Also, I think a boost gauge at this point is cart before the horse. I fail to see it's diagnostic value.
EDIT: and just for the record, how long have you had her, and when was the timing belt done last? Mileage?

I'm guessing loose intercooler piping connection or hole. Have you checked all pipe connections?

After many months of trying to find the problem, I've finally fixed it. At first I checked for restriction in the intake. It was good but I cleaned it anyway. I replaced the MAF sensor, I checked for oil in the intercooler. Nothing. I checked for a boost leak. Nothing. Eventually, I replaced all the vacuum lines but still nothing. When I replaced the vacuum lines I found that the turbo actuator did not hold vacuum at all. I replaced it and went the old part was out I made sure that the vanes moved freely which they did. Put the new actuator in and still nothing. I looked online and found the only thing left that I could think of and that was the N75 valve. I went to a wrecker and got a used N75 valve and a new check valve right aways. I popped it in and I had power instantly. It was like night and day. Before, my car would struggle to get up slight inclines but now I can watch the boost gauge peak at 20 everytime. Very consistant and no longer goes into limp mode. I assume because the actuator did not hold vacuum that it was sucking in dirt and water into the N75 valve and eventually plugged it up with garbage. But now she runs like a champ. Very consistant boost and awesome power compared to how gutless it was before.

Awesome! Good job, and way to stick to it!
The update is appreciated.

Well, did you clean the intake runners on the head too? There is a risk of a puce falling off now that there is more air flow and getting between the valve and the seat and this kills the engine. Its happend quite a few times around here.

My N75 had sucked in a lot of debris from the old, failing actuator also. Good find and thanx for the update.

Thanks so much for reporting back! So the actuator was froze from never operating, turbo ran full tilt all the time.

Good find it's usually vac lines that dont show up in VCDS