Jan,
Unless you have a custom map that someone has created and you don't have a copy of it then the only map you can't write from the RT is the OEM factory map. If you have a pre-existing flash then those are included in the RT.
I know, there are various versions of these calibration files but the ones included in the RT are the latest for the 2 supported combinations and supersede whatever older flash you may have in the bike. If, like yours, you have an older flash that didn't take into account the relocation of the IAT then you need to do that prior to overwriting the older flash in your ECM.
Just relocate you IAT, load the correct map file for your pipe / location, reset the speedometer for 28T and ride. If you have a custom map then simply reload it and set the speedometer flag. It's really that simple.