I believe the dedicated FFV heads were phased out in 01, but I could be wrong.
If the ffvs in your comparison were only available with an auto trans, while the regular 3.0s were available with either transmission, that alone would drop the fuel economy of the FFV trucks, and it's not even engine related.
I went to fueleconomy.gov and compared a 2000 2wd FFV with manual vs the same truck with an auto trans, and the manual trans truck was listed as getting 1 more mpg than the auto equipped truck by the EPA sticker. The users with manual trans trucks were actually reporting nearly 2 mpgs better fuel economy. If we apply that 1-2mpg difference due to the transmission to your regular 3.0 vs FFV 3.0 argument, then the numbers are much more similar.
And if we compare an 01 2wd regular 3.0 equipped with a manual, to a 2000 2wd FFV equipped with a manual, the FFV is actually rated 1mpg better than the regular, and the users reporting show nearly identical fuel economy, with the FFV having a slight edge.
Fuel economy depends on so many variables that it's difficult to predict, especially in a vehicle like the Ranger with multiple platform variations and power train configurations. A base model, regular cab, short bed, 2wd FFV with a manual trans weighs around 3200lbs. If you put that same engine into a 4wd, extended cab truck with an auto trans, and power everything and it pushes the weight beyond 4000lbs. Obviously, the larger, heavier truck will have worse fuel economy.
Either way, for the OPs situation, picking an FFV engine shouldn't matter. Getting an engine in decent shape is much more important than getting a regular or FFV. Other than the fuel injectors, they should be identical, and perform the same.