Mk3 is shown first and is different from mk4 and mk5. The mk6 is probably the same as mk5 cables. Poor shifting could also be improved by changing the gear oil with new oil or using a different thickness oil. Thinner oil will let the synchronizers engage quickly, especially in cold climates.
For tips on flushing the gear oil on a mk3 VW Jetta TDI or Passat, see 1000q:
change trans oil
For tips on draining the manual transmission on the mk4 VW Golf TDI, Jetta, or New Beetle, see 1000q: mk4 transmission oil
For the tricky procedure on the mk5 VW Jetta TDI, see 1000q: gear oil mk5
There is no clutch pedal or clutch master cylinder rod screw adjustment. It is a hydraulic system so there are no cables. If there is poor clutch pedal action it could also be caused by a worn clutch pedal assembly (unlikely), worn/bent clutch slave cylinder rod (unlikely), bent clutch release lever, worn release lever pivot. This assumes the stock setup and not a shimmed pivot or different specification on the flywheel step.
For a review and installation of the dieselgeek sigma 5 short shifter, see 1000q: dieselgeek short shifter install.
Remove the air intake filter box or battery as required for access. A common problem is not being able to shift into 1st gear. Another problem is getting reverse when you shift into first. These may be due to cable stretch and play in the plastic shifter bracket. Loosen the nut (yellow arrow) and move the cable a hair towards the front of the car. Retighten the nut.
Go for a test drive and make sure that you aren't getting reverse when you
shift into first. If so, you adjusted it too far. Just move it 2
millimeters per adjustment.
The plastic shifter linkage has also been known to break due to age and
wear. To replace it, remove the adjustment nut and slip the cable off the
end by lifting the retainer up. If you remove it, grease the pivots.
You can also use a metal replacement that shortens the side-side throw (does not
adjust the fore-aft throw) with a gruvenparts
The factory service manual says that on the mk4 and newer, you have to remove the center console and lock the shifter knob to adjust the shifter cables. This is shown in the video at the bottom. I suggest only adjusting the cable ends because it's easier and faster to pull the spring back and move the shifter cable end forward or backwards 1 thread. If it's still not working then try the method in the factory service manual.
Have a helper move the shifter inside the car while you watch the shifter assembly on the transmission (shown below). Fore-aft adjustment should be the cable on your right when standing in front of the car, looking down, and shown in the picture. Left-right adjustment should be the cable on the left.
On the mk4 you should have enough room to reach in there. On the mk5 Jetta and the mk6 Golf you must remove the engine air filter box for clearance, see 1000q: airbox removal for details. Below left is a mk4 shifter assembly (2002 model linkage shown earlier versions (2000) have slightly different cable ends that the Bentley manual recommends be replaced each time they’re removed from the knobs on the shift levers as they utilise a press fit; earlier designs (1998 New Beetle) are closer to the MkIII design.)
Below right is the mk5 with the battery box removed for
Pull the black ring back to compress the spring (removed for
illustration). This will expose the shifter cable end and release its
threads from the threads on the cable. Move it forwards or backwards 1
thread/notch to "skip" over the threads and then
release the spring to clamp the end onto the cable threads. If you wish to lock the springs in the compressed position, turn the
black plastic ring. This is not necessary if you're just moving the end slightly - just pull the ring back, adjust, and release.
You can also grease the pins on the linkage to make the ends move smoother. Release it by lifting the center tab on the clip. I suggest doing it while it's secured to the cable so that it stays indexed to the cable end.
Go for a test drive and check for proper shifter response.
Here is a video from www.dieselgeek.com showing more details on adjusting the 5 or 6 speed manual transmission shifter.
If you still have questions on how to adjust your Volkswagen manual transmission shifter cable, please post your question in the forum linked at the top and here: myturbodiesel.com .