First, what are you building the duratec V6 for, FI or NA?
What power levels are you looking to reach?
The duratec 2.5 and 3.0 are basicly the same block, just different bore size with a few slight differences. There are a few different options on how to build the engine, so what you are intending to use the engine for will help in pointing you in the right direction.
We Contique owners have been swapping in 3L's to replace our 2.5's if that gives you an idea on how close they are.