Originally Posted by TexaNate
However, last I rode the light started flashing at a rate of roughly one second per flash. Then it went off entirely. Then it came back on again and went back to flashing.
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