First things first, be gentle with me as I have never done meaningful troubleshooting on an EFI vehicle of any kind. I have a Buelltooth on the way, but don't have it yet, so I can't do anything vis-a-vis looking inside the ECM (yet. I will update as I can learn more).

Bike description: 2006 XB9SX, KN air filter, airbox mods done by PO (VC breathers vented to atmosphere, not airbox, via a T from airbox fittings to a small mesh cone filter behind left footpeg), Ulysses muffler box with the valve in shut position. ECM map unknown. No right-side scoop. New correct plugs 800 mi or so ago. Oil change 500 or so ago with 20-50 mobil1 vtwin oil, it's full of oil.

Description of the problem:
  1. First Occurrence

Take the bike out in 90-95 deg weather, run it around on back roads around 60-80 mph. Stop and refuel with 93. Run it some more on backroads, pass a car and run it to 95 or so to pass, 80 after that. Stop, run at 60 for a bit on a 2 lane policed highway. Bike starts missing (how i perceive it)/surging. Pull over, rev it a few times, revs clean, get back on highway, now popping thru airbox, CEL illuminates, power way down. Stop, let it cool (rear cyl fan on for a few mins, maybe 3-5 unsure, didn't time it).

Battery is low so it won't hot start. Bump it off, doesn't want to idle, keep it alive with one hand while putting on gear including helmet (try that with one hand sometime!), get going. Power still way down, CEL illuminated.

turns out if i throttle it way back it feels like it picks up both cyls but whacking it wfo has bad results. Trying to get home so nursing it on low throttle openings seems to help for 5 mi or so, then it seems almost "back to its old self." 5 more miles and it's definitely back to its old self. Park it and resolve to get a buelltooth before I post again. Google... look here... maybe it's overheating and turning off spark because hot?

  1. Second occurrence:

Saturday. Take the bike out for errands after bumping it off (should have charged battery, didn't). Stop, 5 mi later, have to bump it again. Not stopping to get steaks now, this is just a ride around day (also discovered clutch drags during bump-off attempts).

Bike runs as normal, riding again between 60-80 on backroads until i've been On It awhile in 90 deg temps, heat index 100, humid (rear cyl fan is on even in motion). Power feels like it's softening, could be me imagining it... run it at high road speed and low engine speed and it seems to clean up? maybe? Again, i could be imagining things. Get caught in slow (40 mph) traffic behind a prius (of course). Now it starts surging and missing (no backfires, but roll on is VERY weak vs normal). No CEL. Go back to babying throttle. Within 3 or so miles it feels "right" again and then stayed right, though i was on slower speed roads and didn't cane it. Cane it close to home and it's fine.

I've found threads indicating that the real cyl may be switched off into "parade mode" if heat is a factor. Not here, specifically, most of the threads here are "get a buelltooth, read actual data, don't guess [this is good!]. I'm wondering if this is a common failure/limp mode?

That said, i took this thing from Durham NC to Portsmouth VA last year in August in similar if not hotter weather and it was fine (but we were moving rapid the whole time). This feels like a new problem versus last summer.

I plan on installing the buelltooth and RSS next weekend. Thoughts?