Just to add my two cents... I'm a long time BMW owner who recently switched over to Audi. I went 98 328is>99 540i>04 530i to the 2004 S4.
When I first got the S4 I was really amazed how much different it shifted versus my BMWs. On all of my BMWs I had a big ass clutch stop and had the clutch pedal tuned so I can jam it down the clutch to the stop right after the clutch disengagement point. With the audi, there is no clutch stop and the clutch engagement point is much much higher on the throw of the clutch pedal vs BMW. Took me a week or two to get used to this after driving manual BMW's for so long. Also, the audi has much longer throws then any of my BMW's but the shifter is so much smoother, makes for a more enjoyable experience.
What I've come to learn about the S4 is that it uses a completely hydraulic clutch system versus the BMW system which I believe is partially mechanical. As it relates to the shift rod, the shifter is actually "cartridge" based and is very different then any BMW shifter I've seen. Most SSK kits i've seen for the S4 simply replace the entire cartridge assembly. The biggest difference seems to be straightening out the shift rod as the OEM rod is bent and most SSK kits are not bent. I'm not sure if shortening the rod is gonna make much of a difference in shift length. Also bear in mind reverse engages in a lower position then 1st gear so don't mess up the reverse engagement by shortening.
If you are gonna try to mod the OE shifter I would recommending getting a new cartridge from Audi and playing with a second assembly so you can also stick the first back in! Here is a good link from the DIY forum;
http://hometown.aol.com/hyperm3/NeuspeedSS.html
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