Chris,
I don't know if the ECU you have with the Duratec is tuneable but if it is, get it on a dyno and have an experienced tuner look at the mapping.
The ECU on my older Zetec was not easily tuneable so I changed it then had a dyno session. It made a significant improvement in the areas you mentioned.
In general, if you change things like exhaust systems there is a tendency to push the power band slightly higher and the ultimate individual throttle body route (ITB) will significantly improve the throttle response but almost certainly improve the top end power at the expense of low end torque.
Increasing low end torque is actually more difficult than increasing higher end power assuming you don't want to turbocharge it or start playing with head modifications, compression ratios and camshafts.
