When you say the standard R3 140 HP tune, exactly what tune are you referring to? As most here who have been working with these tunes for awhile know, the R3T and the Standard/Classic models have different tables and their tunes are not compatible.
Did you perhaps load the 138HP tune that I helped Wayne at Tuneboy develop? If so, have you done the intake and exhaust modifications that tune was designed for? Without those changes a stock R3T would run much too rich.
There is a considerable amount of knowledge here concerning these bikes and their tunes. Most notable of which is Wayne at Power-Tripp Performance. Unless you have some experience in tuning these bikes I would advise caution when making changes. These tools offer a great deal of flexibility in tuning the R3 but they can also cause some serious problems if applied incorrectly.
Not trying to bust your balls, you may well know much more than I, most do. I'd just hate to see you damage that R3T.