Originally Posted by oldtrucks
The flashing light may not be related to the EXUP removal. If you have the EXUP or access to one you can plug it back in and see if that clears the light. As mentioned there are several means to trick the system and turn off the light. 12 O'clock labs and Graves offer plug in modules that will defeat the light. Others have used diodes at a fraction of the cost.
Without ruling out the EXUP first you're really guessing what the problem is
According to the fault codes sheet, The only reason the light flashes
(rather than just "illuminating" continuously) is as a no-start indicator for 12, 19, 30, 41 or 50 - and the bike wouldn't start if one of those were the problem.
I'll wire up an EXUP plug in module and I'll let you guys know if anything interesting happens.