You can run the stock bore with a stroker kit and avoid all the additional machine work.
Ol' Walter Marcy sure was convinced you could run 2.5L with a stock stroke though, and I will say the man does know his Duratecs.
On another historically siginifcant note, a "cheapie" stroker kit may be available soon. Mazda will be releasing a 2.5L version of the Duratec soon, and shortly after it hits the junkyard it may be possible to do a stroker (or larger bore, I'm not sure which dimension they increased) with all factory parts.
EDIT: Actually my Google searching came up with dimensions. It is both wider AND deeper.. 89 mm (3.5 in) bore and a 100 mm (3.94 in) stroke. Should be here for the 2009 model year... so look for it as soon as 6-8 months from now.