The biggest difference maker in Duratec fuel economy is not based on the year, but on the transmission selected. My 01 Duratec/5 spd truck would get 30mpg in the summer and 28-ish in the winter. Most auto equipped trucks seem to max out in the mid 20s. Lower if you find an extended cab/auto combo due to the added weight.
All Duratec/auto trans trucks supposedly came with 4.10 rear gears while the manuals came with 3.73s. So even if you swap from auto to manual, you'd be spinning more rpms at highway speeds and getting worse fuel economy than a truck that was originally a manual equipped truck. Or you just add a rear axle swap to the list of hardware needed.
Swaps can be done, but you've already gotten decent advice on that in another thread. To make the auto to manual swap the easiest, you'd need to start with both trucks being 01-03 to avoid the digital gauge cluster that was included in 04+ trucks. From there, you'll need the transmission, pedals, PCM with PATS removed or with matched ignition key, shifter and driveshaft.
You have the option of switching out the gauge cluster to one with a tach if you want (it would need to be from an 03 or older truck (any engine type is fine).
The whole swap is much easier if you have a clutch pedal position sensor included in your current dash harness. I know that Ford often included that sensor in most dash harnesses and would simply cap them off if not in use. But... my Auto equipped truck did not have that sensor like so many people said it should, and I had to swap out the entire dash harness.
If you can't find an 01-03 to make swapping simple, and you're stuck with an 04+ truck then you'd need all of that same stuff, plus the gauge cluster, key, and I think the GEM module too. They must be paired together.
Really, it's probably better to just wait for a manual trans truck than trying to deal with swapping from a single donor or worse yet swapping in individual parts.