well I just jumped in last night and figured it all out. After a few mods to the pedal itself, VAGCOM registered the pedal and showed 0 to 100%.
Anyway...perhaps this may help someone somewhere...here is how to do it. Cut the pig-tail off the factory mk3 DBW unit. Find a donor mk4 pedal and cut the pigtail from the harness. My donor was an 01 Jetta 1.8t.
So with the two pigtails in front of you, wire like so.
mk4 pin # (color) -> mk3 pin # (color)
1 - Gray/white -> 5 - Green
2 - Yellow/green -> 2 - Pink
3 - Grey/Red -> 3 - Brown
4 - White/Blue -> 1 - White
5 - Grey/Blue -> 4 - Grey
6 - Brown/Blue -> 6 - Yellow.
After I turned on vagcom I noticed that the pedal registered no lower than 7.5% even when adjusted to the lowest setting. I had to modify the housing on the mk4 pedal slightly to allow the potentiometer to go down to 0.0% After that the pedal showed smooth movement through vagcom.
In the picture below you can see the massive and antiquated mk3 DBW pedal. It looks much worse that this before you cut all the metal away. On the right you see the mk4 pedal. Much nicer package. Above you can see the mk3 to mk4 plug and play harness. The left side was cut from the mk3 DBW unit and will plug right into the car. On the right of the harness is the pigtail from any DBW mk4.
Hope this helps.
Jason