Which Tuner? 99 Powerstroke

[MR5x5]

Damn, I'd have put money on the over boost. You sure the OB reg is working?? I think you can disconnect/plug the boost pressure line and run it that way.  I believe it it will default to a canned fueling table.
Have you tried disconnecting the turbo waste gate?  Disconnect the vacuum line - can run this way always without issue.
Check the oil pressure sensor at the front of the drivers side valve cover area, toward the inside.  Look to see if the connector is full of oil- which would be bad - seems like a stretch, but a flaky pressure sensor can cause weird things.

[Vek]

Oiled cotton like K&N is fine.  Your crank breather pukes oily misty blowby in immediately downstream of the filter, upstream of the turbo.  Don't sweat ingesting whatever oil is on the filter. 

The oiled filters can be problematic on MAF sensors on gas engines. 

[Cylvertip]

Finally wss able to get the truck into Randy's Monday to have them figure out the problem.  it ended up being a slightly loose clamp between turbo and intake.   I got the truck back yesterday. 

 

[MR5x5]

Glad it was simple.

Interesting though, that condition usually blows the boot right off.

[Cylvertip]

Update.   

  Since getting it back it has not been 100%.  It ran great  95% of the time,  but at higher rpm, it would kind of fall on its face and slowly stumble out of it.  Only really came into play when severe lead foot syndrome was involved.  I only put maybe a couple thousand miles on her a year now, and did not get around to getting it in to get looked at.

 Finally got it to Randy's again and they had the issue figured out in short order.  With the turbo wound up, it was sucking the intake tube coming from the filter flat.  It was still the factory original with a K&N filter in it.  Filter was clean.  The added ponies from the SCT programmer probably contributed too, but age and filter oil causing degradation were probably the bigger factor.  They put an S&B cold air intake in.  Back to "you better be holding" on status.

   Glad to see Randy's still going strong.  When ownership changes on a  business, you wonder how it is going to go.  It's been 3 years now.  Haven't skipped a beat from what I can see.  I have been going to them since 2001, when I got this truck  Shout out to them.