In general, hi flow air filters do just that................
They flow more air.
I have had bikes that needed to be re jetted after an aftermarket air cleaner install.
However, I would doubt a year later this is causing your problem.
Have you checked the sparkplugs for lean condition?
You may have developed an air leak. The FJR does run on the hotside, so I would check the rubber manifolds first. An easy check is to spray around the intakes with some contact or carb cleaner. If as you spray , the idle changes.....you found a leak. Manifold leaks are very common on motorcycles as they are subject to high heat and vibration.
Seems a little odd to be showing an FI error code that could be attributed to the filter unless the K&N has dried out. I've had problems with K&N's in the past with fouling of inlet sensors by the K&N filter oil. An inlet leak or poor electrical connection sounds like the first round of checks.