Knowing the mileage is always a nice bit of troubleshooting info.

Regarding your Spyder, and those of others. The 1330 engine design utilizes a coil on plug style ignition.
Using visual inspection for spark plug wear is no longer a viable indicator. Modern spark plugs contain resistors, and as the plugs get miles on them, the resistors will break down, resulting in weak spark, and misfires.

Additionally, the increased resistance, overloads the coils, which often causes them to become weak until they internally fail. Factor in the effects of heat, especially the high heat of a Spyder, and things compound for the worse.

If you read the published maintenance, BRP states the spark plugs are replaced at around 28,000 miles. This is not based on electrode wear, but concerns about the resistors failing.

That said, I highly recommend to replace all spark plugs with Denso brand spark plugs. I know many folks go with NGK. After too many failures in race bikes, I gave up on NGK and run Denso plugs in all our vehicles and race bikes.
It is possible, your coils have gotten weak and may require replacement also.

While apart, you should consider replacing fuel hoses, and these machines also are prone to purge valve issues too.

Regarding the image of the cylinder wall, the cylinders are Nikasil. Rust is not a concern, and unless you had catastrophic failure, you will be fine. Sometimes we scope aircraft engine cylinders. Honestly, the most insignificant concerns appear as huge defects. Engines get torn down, only to find nothing. Not a fan of scoping cylinders most times.

 

I stated the mileage in another thread and sorry I forgot to put it here. The issue appeared at 9600 miles. It has 11k on it now. I was using the plug coloration as a comparison since #1 is definitely different than #2&3. The primary stick coil resistance is 1.1 ohms on all three. Cylinders 2&3 do not look like cylinder 1.
I do not know the maintenance record for this machine. I do know that less than 1,000 miles per year for 10 years might indicate it’s had some fuel go bad in the filter, lines, tank and fuel pump. I replaced the fuel filter after running 4 tanks of premium 91 octane fuel. Had no effect on the lack of power or poor fuel mileage. I added Seafoam fuel treatment to the next two tank fills. It appeared to have some vibration going on at over 3500 rpms. Since I do not know the “normal’ amount of vibration for this 3 cylinder engine and it did not seem excessive. It left me one option, pull the spark plugs, test the injectors, and clean the electrical connectors. In the absence of any “code” and just an inability to go over 65 mph and attempting to maybe go 70 mph, would produce a flashing limp mode after 15-20 minutes. Stop, pull over, turn it off. Say to myself “Here we go again.” When I turned the key on and restart it was gone. There never was a flashing little symbol like for VSS or anything. Just Orange Limp Mode and telling me to take my 10 year old new to me Spyder RT-S with all its accolades to a dealer. I suspect a weak cylinder for one reason or another. Scoping the cylinders is just one more piece of information that might reveal something. Just like a compression test might just tell me something or a leak down test might too. Do I really want to miss something so I can look forward to disassembling this machine again since I didn’t leave a stone unturned. I think not. At least I now have a $13k training aid. Education cost money and I have spent my own money on practical experienced based education for decades. This is not really what I was expecting. And thank god it isn’t an aircraft. Sorry I did not include sufficient information up front. Thank you for your input. A lot of good information on the technical aspects.

 

If you suspect you have a weak cylinder, and certainly it is possible, absolutely do a compression test. As you are probably aware, a cold cranking test is fairly easy, while a differential leakdown is more involved but will reveal more specifics.

Honestly though, these 1330 engines get high marks for reliability. That said there have been folks that did encounter, on newer years, loss of compression which has never been explained in detail, but was resolved by what seemed to be the dealer, making computer adjustments.

Absolutely not here to debate training, or the why so much, but rather lets see if this is something to try and troubleshoot here.

Is this the same Spyder that a couple months back you presented the issues here. Ultimately replacing fuel injector nozzles, spark plugs and more?

So, to gather a baseline, is the Spyder stock? Meaning oem exhaust. No remaps. No Throttle Commanders. No accessory lights or aftermarket trailer hitch.

Your mentioning of the fault, clearing upon restart is one mode Spyders will see happen. The fault should store, but requires BUDS to read in some cases.
Have you ever pulled a code prior to shutdown?
If so, do you recall the code?

I regards to operation, you mentioned vibration. This vibration, to clarify, does it occur almost immediately once warmed up and ridden, or is the operation smooth and at 20 or so minutes begins vibrating?

I do not recall, did you only test the coils, or replace them?
When testing the coils, did you test both primary and secondary windings?
While testing the coils, did you heat soak them while taking primary and secondary readings?

Seeing the plugs, and only 1 showing a richer color has me, and likely you, leaning towards that cylinder being the instigator. Certainly, it could be a mechanical issue, but obtaining a fault code would be a huge help. My own suspicion though, leans towards a failing coil.

I have dealt with very similar on my wifes previous Toyota Corolla. Plug replacement was to be at 100,000 miles. At around 60,000 it began having misfire faults. I did replace one coil, which resolved the issue, until a few months later, a new misfire code appeared. At that point, I replaced all spark plugs, and installed 4 new Denso coils. Kept the other newer coil as a spare. Car ran like a champ until sold a year later. Granted, access was easier, as was checking with obd2. Moving the questionable coil saw the fault relocate to the cylinder where the coil was moved too, validating it as faulty. Again, it remained an intermitent misfire fault code. With new coils and plugs, the mileage improved a lot.