The way I’m reading it, your Stage III was installed, everything ran good and about 5 months ago your bike developed a “knock”, and you’re now wanting to get rid of that knock.
Any major changes since the dynotune? (i.e. weather is significantly hotter/major humidity change than when it was tuned, changes to header/pipes/breather, or consistently purchasing same bad gas from a less than reputable source). I’ll assume altitude is the same.
The dealership would probably have been more conducive to helping had you addressed it as soon as you noticed it, especially if it came on the heels of the tune. It doesn’t sound like they’re interested in helping now unless they’re compensated for their time and labor.
I’m curious, what did they say after you told them it’s been doing it for 5 months, and you’ve filled it up 20-30 times since, at different stations, with different brand gasoline and the issue persists?
Okay, so what are your options? I don’t believe autotune will fix the issue.
If you purchased the tuner from Fuel Moto, call them. They’ll hook you up.
If you purchased it elsewhere, (like your dealership) see if they can’t provide another base map for your bike’s application. Maybe they’d provide you with a more recent map of a similar build as yours or hang onto one for you of an upcoming build.
Try a map from Dynojet’s website. I’ve heard mixed reviews about their downloadable maps.
Call Dynojet. Again, mixed reviews, my experience was good, but in the end they pointed me to a base map on their website that mostly resembled my application. A few autotunes later and my bike ran pretty damned good.
Find someone who has your same setup, and get their map.
Hopefully someone in this forum who knows what they’re doing can walk you through via email or phone call. There are a few in here who are very competent.
Lastly, take a look at this. If you don’t know what your doing, call Dynojet after you’ve tried to understand the instructions as much as possible and see if they can’t walk you through the process. You have the right tool to fix your issue, it’s just a matter of knowing how.