2006 FZ1 ROUGH IDLE AND MISFIRE?

Hey all, new here (just got the bike about a month ago).
I went for a ride on Sunday, all was well. Yesterday, I took the headlights and front faring off along with the gauge cluster (I was testing the voltage to the headlights because i keep blowing the drl fuse). I started it with all that disconnected and it ran so poorly. I put it all back together and took it for a test ride but it felt like it was just on maybe 2 cylinders. I didn't push it hard but as soon as I hit like 6k rpm, it smoothed out. When the revs fell, it ran choppy again.
Any help would be appreciated! I'm hoping someone can direct me to another thread that might have the answer. I can attach a video if that helps! Mods on the bike include: throttle commander auto tuner, egr delete, and a slip on muffler.
 
Have you done any maintenance on it? I dont have a gen 2 but i bet the plugs and a strong battery are critical to it running right. Im also critical of any modern fi fuel filter as they dont allow water thru, and the basic function of FI compounds the importance of having a good fuel filter.
 
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