Out of warranty, my guess is that it would be on a time and materials basis. I suspect the warranty book rate is quite unrealistic for the time it actually takes for a trained tech to do the work.
If it is replacing the full main wiring harness, that is not a simple job obviously, and it may involve a lot more than just getting the panels off. Bearing in mind that most shops for bikes these days charge $150 per hour, and that I would expect it to be a multi-day job from just looking at my Spyder.
If the tech is competent and the dealer is historically fair and reliable, then the cost will be the price of the harness plus their actual shop hours to perform the work, which is fair, no one works for free.
Realistically, you are probably at their mercy. You might ask them to quote a ceiling, but in reality, that would make it very tempting for them to then come close to that no matter what.
I would be very curious as to how, if they could diagnose it to be a harness problem, they could not just repair the faulty part of the harness? To my mind, if a tech has the skills to perform such a diagnosis, which would be far from trivial and would have to be very specific, then I'm sure they would be qualified enough of an auto electrician to expedite a suitable repair. It's not like the dealer has a BRP Harness Test machine sitting in the corner of the shop waiting for the once every ten years a Spyder comes in with a defective harness. I had an electrical problem on a 2016 Jaguar a couple of years back, where if they had replaced the whole harness to fix the problem, it would have probably totaled the value of the car. The main dealer fixed the fault by other means and even warranted the work. I know, I know, a Jaguar with an electrical fault, who would have known the chances of that?
I hope it all gets fixed for your ride. Maybe if you talk nicely to the dealer, they may have a demo bike to loan you for that time to ride? I mean, it is for a charity, and you are potentially throwing a few thousand dollars their way and they can always put their dealer advertising on the bike. Cheap advertising exposure for them I would have thought, lots of people going "what's that bike?", and there are the dealership details! I'd go and have a nice chat with the Sales Manager, buy them a coffee, and see what they can do for you; you never know.
