The VW tool is well and good, although, it does not control the amount of shift rod shaft (the other issue/source of adjustability) in relation to the clamp (the circular clamping for at the most forward aspect of the shaft.
My rule of thumb here is to ALWAYS either measure, mark, or at least pay attention to how much shaft was protruding "forward" of the clamp before disassembly. A lot of times, there will be a sort of line of "demarkation" where the shaft was "clean" under the clamp and where all the engine oil drippage and dirt soil and darken the shaft (where the shaft was exposed prior to disassembly).
Generally when I put one of these back together or assemble a car from scratch.....this is only a guess....there is like 3/4 of an inch or so protruding forward of the clamp. This would be a good place to start. Because, I think THIS is YOUR problem.
You've got to start the WHOLE process by loosening the clamp to take all clamping force off the shaft and then (from under the hood of the car) reach in with your arm and hand and "zero-out" the under hood shifting linkage to the best guess of "center of neutral.".....and start the process from there. And, yes, have the special VW tool in place at that time.
I can't do a better job explaining than what I have done. It is a common-sensicle sort of process best comtemplated with a warm beer and a half-eaten hotdog in your hand........