3406E Miss

My 5EK 3406E is running fine except that when I take it up to 2000 or 2100 RPM and let off and shift it misses for a few seconds after the gear change before it starts running fine again.
It does this empty or loaded. Anyone ever seen this?

 

I usually never run it there but I got in a situation that I needed to stretch it out so I took it up there and that's what happened. (10 speed)
I normally shift around 1600-1800 loaded but this was a special case. When it did it it surprised me so after I got unloaded I tried it again empty and it did it empty too.
It doesn't miss while going to 2100 but it misses for a few seconds after I let off the throttle before it picks back up in the next gear. It actually feels like it's a completely dead cylinders for a few seconds.
No big deal I guess. The truck runs fine and the motor is very smooth power wise it just doesn't have a huge amount of power. I have no idea what it's set at. I've never been able to get anyone to run the number. 5ek51510
It must be about 435 or 455 I'm guessing.
Water Temps between 190 and 210 all the time.
No or very very little smoke.
I think the pyro is wrong but it says it never gets over 700. Straight pipe.
It makes good boost and it makes it early. (25-30 psi )
Makes about 8 to 10 psi on the jakes

 

You better be down shifting this one around 1300 rpm or you are going to drop like a brick. 1250 minimum and then it better be a quick down shift.
I'm always at 80,000 with this combo.

 

No check engine light at all.
Filters are new.
The fuel lines look bad honestly.
I was noticing that yesterday when I walked around it.
I will change them in a short order.
It runs great other than that little hiccup after a high rpm shift.