My answer is for 2002 as that is what I ride. The FLH/T EFI bikes have a 24 tooth Engine Sprocket and a 37 tooth Clutch Sprocket whereas the Carb FLH/T/S have a 25 and 36 respectively. This is an EPA thing. HD believes they can better manage emissions with the EFI and lower fuel consumption hence the slightly longer overal ratios for the Touring EFI. For the softails EFI and CARB are the same - both have 25/26. Street bikes.
25/26 is also the Export configuration.
EFI and carb FLH/T/S are the same for transmission sprocket and rear Wheel - 32 and 70.
The difference at the Engine and Clutch results in a fifth gear final ratio of 3.37 for EFI and 3.15 for Carb touring Bikes.
They want to sell EFI bikes as there is much more money in them for factory and above all dealers over the life of the bike. Hard to do if they get their clock cleaned by a less expensive version of the same bike.
With the lower gearing at least they can hang in there close enough to where most people will not notice.