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There are a number of problems which can cause engine hesitation and poor running, please see 1000q: limp mode fix and 1000q: constant low power fix for other possible causes. This article only deals with the mk5+ turbo hesitation and poor response.
The turbo on all mk4+ TDI engines is a variable nozzle turbo (VNT) which uses vanes that point at the turbo to adjust the turbo boost. Below is a video showing the basic parts. If the stop screw or rod is adjusted incorrectly, the vanes will close too much and choke the airflow or open too much and cause poor turbo response. This engine surge feels like turbo lag followed by a torque spike. The vane adjuster ring inside the turbo can also wear, causing similar problems. In my case, the engine had a lag and some smoke up to around 1500-1700 rpm and then a little jerk of power around 1800-2000 rpm. I believe there was a little wear on the vane adjuster ring against its lever or some other mis-adjustment which caused the vanes to close too much.
This problem is unrelated to turbo compressor surge (blade stalling) which is caused by a high load, low flow condition inherit to a turbo's design envelope. A misadjusted stop screw a spike of torque as the engine recovers from faulty vanes or vane position.
In some cases, this symptom has been noted with EGR valve failure. If VNT stop screw adjustment doesn't help, a simple test is to block off the EGR gasses with a piece of sheet metal. An aluminum can will work for temporary testing purposes. This will throw a check engine light but if the problem is fixed, you isolated the problem.
When I logged boost actual vs. requested and engine rpm, I saw some hesitation and response issues as well.
Here is how a VNT works on the inside and a description of the problem at the end.
Parts and tools
vacuum gauge and tester
3/4" extension and universal joint
3mm allen wrench
VCDS cable from ross-tech.com
First check VNT function. Read 1000q: VNT actuator adjustment for background on how it works and how to adjust the actuator. Mk4 shown, mk5 similar. There is currently no direct replacement for the BRM engine turbo actuator but the CBEA/CJAA actuator can be made to fit with a custom bracket. It is usually set correctly from the factory but the spring or diaphragm inside can weaken or tear.
To confirm that stop screw adjustment is needed, you need VCDS. Warm up the engine to normal operating temperature and then turn off the climate control/air conditioning.
Plug in VCDS and enter engine module, then basic settings, then use the test "charge pressure control" (group 11). The engine will rev up to 1400 rpm and then the computer will cycle the boost. The boost pressure should go up and down. Anywhere from 80-250 difference between the high and low boost is normal. Too low or too high and engine response will suffer
If the boost difference is too small (unusual), shorten the stop screw. If the difference is too high, extend the stop screw to restrict VNT actuator rod travel.
Raise the car, chock the rear wheels, rest the car securely on jack stands, and make sure the car is safe and secure before doing anything else. I use 2 sets of jackstands, minimum - one at the factory jack points to carry the weight of the car and another almost touching the front subframe as a backup. Also see 1000q: wood blocks for another idea of supporting the car.
Remove the plastic splash shield under the car. It's held in place with
8x T25 torx
screws indicated by the yellow arrows below. The rear is held with 3x T30 torx
screws (white arrows).
The turbo stop screw is between the block and oil line. A 3/4" extension and universal joint with a 10mm socket is required to get to it. While you're under there, inspect for soot leaks by the EGR cooler valve. I removed the silver envelope heat shield for access. First loosen the 10mm lock nut and then use a 3mm allen wrench to turn the screw 1 turn clockwise (lengthen the rod in relation to the lever) and repeat the charge pressure control test. If it needs further adjustment, move it in 1/4 turns to fine tune. Repeat until the boost difference is in the 80-250 range and recheck after you've tightened the lock nut.
Here is a view looking at the rear of the engine with the intake manifold removed. (top of picture is up)
In my case, the threads were covered in rust and snapped as soon as I applied any torque to the nut. If this happens to you or you want to do the adjustment the easy way, don't bother getting under the car.
The easy adjustment is to use a plastic zip tie to restrict rod travel length. Simply use your vacuum gauge and apply vacuum to the VNT actuator nipple. This will extend the rod all the way to the stop screw. NOTE: This applies to the Borg Warner turbos found on the BRM Jetta engine (and later similar turbos). If you have a mk4 engine with a Garrett turbo, vacuum causes the rod to shorten. Loop a zip tie around the lever at the bottom and the nipple at the top and then tighten the tie. Release vacuum so the rod is retracted, then tighten the zip tie 2 clicks. Retest charge pressure control and adjust the zip tie length as needed. I suggest wrapping the bottom in foil before looping it because mine melted after 8 months at 1 tiny spot (suggesting it touched the exhaust side of the turbo).
If it doesn't smooth out your engine hesitation at least you know the stop screw doesn't need any adjustment. Check EGR function and other items on the low power/limp mode FAQ and checklist.