Easiest way would be with the adapter Sky showed above. Or get a rear set that changes the shift lever mounting position like the Evol Technology rear sets that you can order in GP shift. This will let you install them and keep the sensor in STD shift so you don't have to do anything with the ECU but lets you run GP shift by way of changing the mechanical input/leverage to the sensor itself.
If using the commonly available ECU editing softwares out there they should allow you to change the shift sensor direction if you go with a rear set option that requires flipping the sensor itself. Or if using the KRT FI Cal software, under parameter list item 46, you can change that value between 4 or 5 to change the sensor direction.
So you have options either way, it just stinks because you're going to have to spend a few sheckels to make it work. That is one of the things that Yamaha did that I applaud with the 15+ R1 was the pretty trick 'feature' allowing the OEM rear sets/shift lever to be drilled out and tapped to easily change over to GP shift.