Duratec definitely.

I assume you're looking to keep the bottom end stock?

Forget the head work unless you're aiming for 220+hp. The ports are massive (even bigger on the 2008+ heads) and stock valve size is more than adequate.
No no need to change the inlet at all unless you want more than 180bhp. Any more than that and I'd look at the inlet Mountune developed for the Fiesta ST. ITB's don't come into play until you're looking at over 230hp.
A good intake manifold, exhaust and some mild "fast road" cams will see you close to 200hp with excellent drivability.
Gearbox choice is more limited compared to the zetec. You have either the IB5 as fitted to the Fiesta ST or the MTX75 in the Duratec 2.0 focus - not the early Zetec MTX's though, as the Duratec has a different bolt pattern on the bell housing.

The best out of the box Duratec/MZR is the engine fitted to the 2009+ MX-5. These had VCT and a forged crank. You pay a premium for these obviously.

Mazda parts are interchangable with the Ford engines, so VCT is an option if you use an MX-5 head.

As for ecu choices, if you're on a budget and not bothered about VCT, something like an Omex 600 or DTA S40 will do the job nicely.