Call AEM, see if they sell a plug and play AEM EMS ecu for Duratec (like the one in HONDA S2000).
They sell different plug and play ecu for many different brands.
Unplug the stock ecu, plug the Aem ems off you go!
Save the original stock configuration before you supercharge the car. It will be easy for the tuner to play the air fuel mixtures and other parameters.
Make sure the injectors & pump can supply enough fuel during boost - before going to
a dyno shop.
Motec, electromotive & other standalone are nice product but expensive. Requires a lot of knowledge wiring, using what sensors, and time consuming dyno/mapping.
What supercharger are you going to use?
I like the compact Rotrex.