No doubt we all have variations in our setups but I haven't ever heard of the need to grind any section of the shift linkage. I'm guessing that you are absolutely sure that your whole linkage setup is from the one variant. One of the lessons I learnt with Audi is many jobs are difficult, so not refurbishing stuff before installation has the potential to be a major PIA.

I have a number of Audi with manual gearboxes and while the standard setup can be a bit long throw and soft with the clutch, I can say they all work perfectly. Add a short shifter and a properly designed clutch and they still work perfectly. The point of the comment is that if the correct parts are used, you guys really shouldn't be having the issues with the 01E shift that you are having. It's really a reasonable setup and although there are better boxes and shifts out there, it can be made quite respectable with a short shifter and +15 clutch. All the JHM upgrade parts are supposed to be good and I have the full internal and external catalogue in my spare box but I have yet to install it so can't say for sure. The car I'm driving today has the straight from factory box with short shifter and +15 clutch and 290,000 Km up and it's just fine. All gears are available without any baulking or any of the issues that are being raised on here.

Fingers crossed that you can put your finger on the cause and get to enjoy the car.