06 Jetta stumble under heavy load

I really need some help with this one. I hope someone out there has seen this before and can help.
I have an 06 Jetta 5 speed. Most of this work was back in May but the owner has only put about 2k miles since then because of surgery. It came in and needed a cam and wasn't running right. So we put in a cam, the injectors were almost at max deviation so we put in new ones, and a fuel filter. Also put in a clutch and took egr out. Car seemed to run fine and owner was happy. About a month ago the number two cylinder started misfiring. I was told to swap it with number one to see if it followed, but that it could fix itself. I was skeptical. But I did that and it actually did fix the misfire problem. However now under heavy load the car stumbles like its not getting fuel. So I found the in tank pump not working. Put a new one in with no change in the stumbling. Couldn't get a good reading on the fuel pressure at the tandem pump so I tried a new one that didn't help, so I reinstalled the old one. I also unplugged the intake flap motor to see if that might help. Last resort was to try to warranty the one injector that was misfiring. Just did that and its still the same. There are no codes other than a bad glow plug. The car seems to run just fine until I ask for boost mostly in third and fourth gears under acceleration it stumbles.
I think I have covered all I have done. Anyone have any ideas? I will take all the help I can get.
Thanks

Check boost requested and actual while driving. Do a run with it chart recording.

I will give it a shot. Hopefully later today.

Finally got a chance to run the car and hook VCDS up. I hooked up I ran the car and it stumbled quite well so but I wasn't running a graph. I ran a graph to see if I could catch it stumbling. I couldn't get it to do it after 20 minutes of driving, So I will wait a bit and try it again. I did notice at times as I was just cruising with my foot lightly on the pedal. The yellow actual line was separated from the green by quite a bit, then settle down. I didn't catch that screen as I was waiting to see if I could catch the other. I really need to get better with VCDS.

I did pick up another code finally.
Intake Manifold Flap Position Sensor (Bank 1)
Could this be fluttering and causing the stumble I'm getting? Of course I just took it out again and its not doing it but Something is going on.

The EGR maybe sticking and flooding the intake with exhaust.

Trying to schedule normal job and this is tough. Finally got it to fail really good the other day. It always faults number 2 cylinder misfire. Talked to oilhammer and he said to look for a wiring problem in the harness. I pulled apart the 14 pin connector under the air box, T14a, and found oil. Found it in the manual I think the oil came from the oil pressure gauge. Electrical is not my strong point so I'm struggling. Any one have any ideas about that connector? Could that oil be causing a problem with the injectors or did I just find another potential problem? I'm still looking but I don't think it has anything in particular to do with the injectors.
Thanks.

Took the wiring apart today and did a continuity and resistance check on the harness inside the head and from the connector to the ecm. Nothing changed and resistance was good. Its only faulting the number two cylinder and when it starts missing if I shut the car off and start it back up it goes away for a while then comes back. Could I still be looking at a bad harness inside the head since its really hard to shake down the wiring inside the plastic rail? Or could this be an ECM? Thats what I'm afraid of at this point.
Thanks

Took a while and basically just trying some things including throwing parts at this problem. After much TS and checking wires. Even though the injector harness checked good, before I replaced a computer I figured to just change it and see what happened. It was the problem.

Try a new fuel filter. I just had a similar issue in my 05. Stumbled under load. I was just about to put in new injectors and a cam. I had recently changed the fuel filter (3 months, 5K miles ago) so I did not think this was the issue. Turns out the fuel filter was the issue. Probably got a bad tank of fuel. Throw the $25 at it before you go any farther.

So was this harness the one that connects to the number two injector? I have read about such problems here regarding the PD.

yes it was the harness inside the head that hooks to all four injectors.