The 2.8 24v makes about 150kW; the 3.2 177/184kW (Mk4/Mk5 respectively), but is significantly 'torquier' down low. All these figures will vary depending on the exhaust configuration you use.
It's not hard to bump the 2.8 to around 165kW and the 3.2 to around 200kW with very minor mods. If you're just after performance, I'd consider turbocharging the 12v VR6, but if you're after a genuinely soulful engine, fit the 3.2, using a complete R32 donor vehicle (preferably a Mk4 for a number of reasons). The cost of the engine swap route will be considerably more than a VR6-T if you don't open up the VR6 engine (i.e. you only drop the compression using a spacer plate), but if you rebuild it with forged internals, then the $$ will add up meaning the cost of both options will be much the same.
If it were my car, I'd fit an R32 engine, as I prefer NA, but it depends where your preferences lie
Fitting the 2.8 24v over the 3.2 is hardly any different. They both use drive-by-wire and come from Haldex-based donor cars - the decision just comes down to the purchase price of the donor car etc.
No engine conversion will be cheap if you pay someone to complete it, though.
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