I got the one with a gear indicator because i have an 03'. But in the instructions it tells you what the diffrent settings are for. Not sure if the X TRE is the same as my A TRE but I would kinda assume they are. Mine says:
"-" is TRE not active
"4" is 4th gear map is used*
"5" is 5th gear map is used, recommended for GSXR1000, 1300
"6" is 6th gear map is used, recommended for other modles (600, 750)
"7" says special mode to bypass 180km/h limiter on Japanese models
*sounds like "4" is mainly for bikes that only have a 5spd gear box, like M109R and VStorm 1000.
Basicly for you, you want 5 or 6. They are basicly the same, except on some bikes 6th gear is governed to 186mph and in 5th it is ungoverned, so you choose. From what I understand on the GSX-R's the timing is retarded in 1st - 3rd gear, and maybe even 4th (havnt found out for sure yet). So basicly what it does is trick your computer into thinking your in 5th or 6th gear all the time so it will use a higher performance ignition map.
I didnt really notice much of a difference when I put mine on, wasnt that impressed. Seemed like it smoothed out low RPM/low throttle cruising a little - less jerkey. But I didnt really notice any power gain.