Hi f4ri4,
There are some differences between these two generations, at least for the Audis, where most of my experience lies. I am guessing it translates more or less to the Passat, but I'm not sure. You have a 3B Passat, and are dealing with a 3BG donor?
There's the type of fuel cooling: My car has an active setup, with a fuel-to-coolant heat exchanger on top of the fuel filter, an electric pump and a separate radiator with the same placement, but on the opposite side from the intercooler. The B6 has a passive setup, with a radiator that the return fuel passes through, under the car.
Then there's the additional heating scheme: The B5 use heating plugs in the coolant (in a small housing beside the tandem pump), where the B6 use a PTC element for heating HVAC air directly.
These differences (and maybe more that I don't remember) means you will have to swap the wiring harness over from the ATJ to the AVF.
There may also be differences in the immo versions between the generations. If that's the case, the "new" ECU won't program to your instrument cluster.
You can get immo removed from the ECU (like I did), or you can get the AVF files put on your existing ECU.
I am currently trying to do the latter, to get rid of the flashing immo light and to put a new tune on it.
One more thing: I had to pull a relay from under the dash on the drivers side. This was constantly clicking, as the "new" ECU was trying to PWM control the electric cooling fan. Without the relay, it seems to operate like normal for the B5.
Eivind