The differances between the D2 and D3 are mostly the ancilliary components, exhaust manifold, turbo, aircon pump and belt drive, breather system etc, etc so I think the core engine would fit using your old ancillliaries. However, having said that I would still advise getting hold of the correct engine simply because the engine itself is actually very strong and reliable indeed. It has three main failings and none are to do with the engine, all are to do with ancilliaries.
1/ As you know already, the swirl flaps can fail so are best removed. This is probably the single most popular reason for requiring a replacement engine.
2/ The breather on early engines require regular changes so are best replaced with the later vortex type unless you stick to annual replacement. This blocking can cause turbo bearing failure.
3/ The exhaust manifold is made of tin foil (only weaker) and best replaced with the E39 cast iron one instead. This does not normally damage anything except maybe the MAF + Air filter.

Granted the EGR needs cleaning once in a while and the DPF can be a pain if the car is a town car but the basic engine will easily run to 250,000 + once the above three points have been addressed, given regular oil changes of course.

I have a very strong feeling you may need a new turbo too so buying as one lump might save some hard earned. Check your old turbo exhaust impeller. my money is on it having chipped fan blades, just one chip will form a crack later on and the impeller will self destruct, it has to be visually perfect.

 

Thx very much for the rapid reply and the very helpful information (the tin-foil description especially )
The heads-up on the turbo is very timely too ..