The XR2 not only has a taller 5th gear but a taller final drive too, 3.85 vs the F's 4.105. My numbers are a little high but not unusual.
The N/A has shorter gearing to make the car feel peppier at the cost of top end, and it does have a small effect on overall economy it seems.
The ECU's & ignition timing are the same between both N/A engines, so that's not affecting anything.
Since your car was originally an auto, you have 9.0:1 CR (n/a manuals had 9.4:1, autos were 100hp and manuals were 116hp) and a different exhaust camshaft tailored specifically for low end torque. Grab an exhaust camshaft from a manual car and drop that in there, your powerband will feel a lot better and more natural with the 5spd, and your highway speed volumetric efficiency will shoot up and increase your MPGs as well.
I have a line on a tubular header, if you're interested PM or email me