This is solved now but it took me 3 years and $2,500 before I finally got it right. Figured after all that, I should share the knowledge in case someone else is having the same issue.

Note to the site admin. You may move / reuse / edit / whatever you like. Figured that this was worth others knowing.

For 3 years I have been fighting the same frustrating issue with this bike. It runs well around town but will randomly start misfiring at interstate speed while cruising. Cutting the throttle OR going to WOT returns the bike to normal mode for a minute or so and then it starts misfiring again. Issue occurs between 3300 and 3700 rpm. I got a lot of good advice from the forums on where to look but this one seems to have stumped everyone.

Well I finally solved this issue and from what I read, there are a bunch of other users with the same general issue that cannot find a resolution. I feel confident that I got the issue fixed this time as I have gone 3 months and 1,000 miles with no issue. So to save others the time and money, here is the history, hypotheses, and fix. It is a bit of a tale but read it so you know what DOES NOT work.

When this started (2016) I would occasionally (not always) get the following codes:
13 Oxygen sensor
15 Intake air temperature sensor
14 Engine temperature sensor
16 Battery voltage
21 inter active muffler control
36 fan voltage

I installed new battery, O2 sensor, air temp sensor in 2016. Bike worked for 1 week then issue returned. Near winter so I parked the bike.

In 2017 I tested the fuel system and it seemed that fuel was being delivered properly so I guessed that the issue was electrical. Installed new plugs, wires, coil. Did a full test on the charging system (generator and regulator) and they passed. Replaced regulator anyway as it had surface damage (rock strike I think). Bike worked for 2 days then back to the same crap.

A few completely useless dealer services resulted in new plugs (again) and a re-flash of the computer (and a lot of $).

Did a complete wiring harness test (puled all the connectors, checked all the wires, checked the computer connections, ….). Found a few small items but nothing that fixed the issue. It occurred to me that the exhaust valve opens and closes at this rpm range and the muffler was rusted (35,000 miles). So I disconnected the exhaust cable and jammed the valve open. Exhaust servo was free to rotate. No effect – same problem. But I could not rule out an issue with the exhaust servo itself.

Contacted KD Fab and got a drummer muffler (NO STUPID VALVES) and an IDS computer to match. KD was really helpful with good quality work. I knew I had this fixed now with a new muffler, computer and no servo. WRONG. Bike worked great for 2 days and then the misfire issue started all over again. But now the only errors were:

13 Oxygen sensor
15 Intake air temperature sensor
14 Engine temperature sensor

During 2017, I had noticed that my oil level was growing slowly during all of this so I thought that maybe the pressure regulator was pumping gas into the oil and (maybe) not supplying the injectors properly. The bike had 35,000 miles so it was probably due for a pump. It also seemed possible that I had an intake air leak that was vibration dependent or the TPS was shaking at the right frequency. Remember, this only occurred between 3300 and 3700 rpm. So I had a new fuel pump, regulator, throttle body (with new injectors, TPS, and seals), new plugs, and a new O2 installed. The plugs and O2 were in case the misfiring had fouled the last set. Bike worked great for 1 week then the same problem again.

At this point I was considering the bike for scrap metal. $2,500+ in parts with no success. That said, all the parts I replaced were worn after so many miles and it was not irrational to replace them. Plus I knew a few were bad (fuel pressure, the first O2, ….). But what could possibly be wrong with this thing?

I went back to electrical (through shear process of elimination!) and thought about the errors, all three were from sensors on the same section of wiring harness. The O2 and engine temp are also single wire (duplexed signal) so any loss in battery voltage / circuit conductivity would cause them to appear failed. I clipped the sensors out of the wiring harness and built a new harness for these sensors that then spliced into the connectors at the computer. The original wires were taped at both ends. I knew I had to have the issue now. I had all new parts and new wiring to the sensors that were throwing codes. Test rode the bike and ….. FAIL!!!! Same issue again.

More thinking and screaming at the bike led me to suspect that there might be a ground issue. I had already checked this multiple times but I did again. No loose grounds. But what if the computer was not grounding well where I could not check? This was obviously a vibration issue where something was shaking. So I figured adding an extra ground would not hurt anything. I spliced into the black wire at the computer terminal (that is the ground wire for the electrical system). I made a connector for the splice and bolted it to the negative battery post. Now the harness was definitely grounded. AMAZINGLY - PROBLEM SOLVED.

It has been 3 months and 1000 miles trouble free. No, the bike has not burned down. No, the bike has not blown fuses. No, the bike has not fried the IDS computer. All seems well. So the hypothesis is that the computer itself is losing grounding when shaking (do not have an explanation for where / how). Now I do not fault the computer as TWO computers have been tried without success . Remember that I ohm tested all the grounds to the computer while shaking the harness 2 years ago and again this year. I never found a loose ground or a break in the wiring that would affect this (did have to re-wire the head lights as a separate issue). I also added a foam stopper on top of the battery to keep the seat off the computer connectors in 2016. As best I can tell, this is an issue with how the computer is grounded / seated.

If anyone has an alternate hypothesis, please add it. But I can tell you that multiple people have gone through this bike and not found the root cause (including me). Adding a ground to the wiring harness at the terminal (total of $0.12 in materials) solved what $2,500 had not. So, if you are one of the poor souls with a cruising speed misfire that cannot be eradicated, just try adding an additional ground to the computer. It cannot hurt anything.

Side note: I do believe that the stupid exhaust valve and servo (thank you California pass by noise) were an issue. I suspect that some of the codes I was pulling were real servo codes that just happened to pop up during a ride that the ground fault occurred.

O2 sensor 3 replacements
Air temp sensor
Engine temp sensor
Battery 3 replacements
Ignition coil
Plug wires
Pugs 3 sets
IDS computer
Throttle body
TPS sensor
Fuel pump
Fuel regulator
Fuel injectors