The gen 3 is a bit different than the previous ones but the the second setting is the accelerator pump function and any setting other than "0" on any of the first 3 settings is adding fuel over and above the base map in the ECM. I don't believe you can remove any fuel regardless of the setting you use.
Just spent some more time on the website (EFI Controllers - Electronic Jet Kit - Motorcycles, ATVs, UTVs, Sportbikes, Snowmobiles, Watercraft, Dirt Bikes) and reviewing the instructions that came with my TFI.
According to their website, the GEN 3.5 TFI is able to subtract fuel from the stock setting. Not quite sure if I understand how this happens with a piggy back TFI like this one.
The included instruction sheet says, "Light settings for GEN 3.5 controllers below 3 are SUBTRACTING fuel from the STOCK fuel level."
Given that this is all true, by following their recommended settings, I'm running barely above stock in Mode 1 (cruise fuel) and stock in Modes 2 and 3 (acceleration fuel and full throttle fuel) and still seeing a large drop in mileage!
My bike is running fine and I didn't notice the drop in mileage until the interstate cruise home from Biketoberfest. But now I'm worried that I'm running just as lean as stock or worse since I've done the Stage I.
Needless to say I'm as confused as ever over this. Sure hope someone from Dobeck can clear this up for me soon.