so if you have a R1, you cannot have any fault codes stored or it will cause issues when it's flashed. this was what had mine all screwed up. don't throw away any sensors you remove like the exup servo and intake flap etc. it will not allow it to be flashed correctly with these issues stored in memory. or if you try to return it to a stock map.
so it may have been my fault. they assured me nothing changes with the software updates they just add new bikes to it. so he walked me through it. I thought i had my kill switch in the run position. on the new R1 the kill switch is also the starter button. it has off, run and push it to start. I thought it it didn't matter which position it was in
so the code 50 was because of that. once I got that figured out another code came up for the exup servo. on the new R1 you cannot access any of the menus unless you clear the codes. so thank god I never threw out my servo motor. I had to take some of the bike apart to get to the wiring i tucked up. once plugged in and erased the bike flashed normally.
I really thought it was fucked up. it would be nice if woolich opened up their forums. this could have been posted and saved others a headache if they did this little oversight of the kill switch on the R1.