Well, it's a completely different thing though. On the B5 our speed sensor has a certain number of "pulses" per wheel rotation. Let's throw out a number and call it 20. Cool. And that 20-pulse signal goes directly to the cluster. Awesome.
Now on the B6, they are using the ABS sensor. It has a different number of pulses. Let's call it 30. That 30-pulse signal goes to the ABS module. Then the ABS module sends that to the cluster. Perhaps converting it first to the 20-pulse type signal, but it might even be a digital signal or something weird.
So the signals are very likely to be different and they go different places. I don't think it would be very easy to make it work. If I had to make it happen I might look into scavenging the ABS module from the B6 and wiring it up minimally just for speedometer duties. Something like that. I think the easier solution is to use the 2003 or earlier 6MT which has the speed sensor. The vin-split is exactly at the 2004 model year.
Please note: the above is just uninformed ramblings, so don't take it as gospel. The numbers are just for the purpose of the conversation and nothing more. It's entirely possible this is a completely easy problem to conquer and has been done before.
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