We never had any of these engines here in North America (officially at least) so expertise here on this forum is pretty thin, given that most members are in the US and Canada. There may be UK and European groups that would have more to add.
That said, some of us have seen them and dealt with them. My impression is that the base engine components are the same or at least interchangeable all the way from the earliest engines to the late series with rollerized valvetrain and upgraded heads. There *may* be some differences in internal components between the "low horsepower" (150hp) and "high horsepower" (163-180hp) versions for each series such as pistons and compression ratio. I believe most components are the same and the main differences throughout the entire range of the 2.5L V6 have to do with fuel pumps, injectors, turbos (hi/low HP), and then the change to roller heads for the "Bxx" code engines. Emission system components also changed along the way -- some have EGR coolers and electronic throttle flaps whereas others done, for example. Finally, there were various different engine control system iterations (early MSA, later EDC) and different ECUs and wiring harnesses to go along with them. But probably all of these things can mix and match if you know what you are doing. I do know for sure that folks have done the conversion from sliding finger to roller heads on the early engines and that is doable with no struggle.
Bottom line, if I had to guess, I would think if you wanted to change engines you could accomplish that by taking the low mile engine (which, if out of a B6 platform car, would probably be a late roller cam Bxx motor) and then transferring over all of the external components from your existing engine: wiring harness, turbo, exhaust, inlet system, etc. Not certain about fuel pump and injectors compatibility -- you would need more research there.
HOWEVER: I would also think about another point. If all that went wrong with your engine is the injection pump and the engine ran well otherwise, why not replace the failed VP pump with much less work and just continue on with your current engine? Did you have any concerns with compression, oil use, operation, etc? If not, keep in mind that the engine you have now is a known quantity that you can speak to the maintenance and functionality of. Any used engine is a gamble. It might have lower miles but you have no knowledge of its past upkeep or any issues it could have. If it's been exposed to flood damage then you have that huge variable in addition.
TDI engines, including the V6, can last many hundreds of thousands of miles with good care. The only inherent question mark on the early AKN-era V6 engines is condition of the cams and followers, depending on how well they got regular oil changes. You can look at that easily enough, and replace if needed, or even change to roller heads from the later donor motor if you really want to dig into it. By keeping your existing engine you also avoid any questions about compatibility with a different year motor and its components. The AKN is already a high-output 180hp version so a nice place to start. If it's in good condition at 200k, which it easily could be, then you could upgrade the IP and injectors on it and tune for them, and have a very nice running setup.
Just some thoughts. Mainly, envious of your B5 with a factory TDI V6! Keep it going one way or another.