I feel that it's entirely unfair to look at ads now that the season is over. Nobody wants to buy a bike in winter just to store it in the garage for several months, so prices will naturally drop. And by the time you could ride it, it's essentially a full year older than at the time of the accident, since riding season here doesn't start until May or so.
Let me restate this. You can buy a bike locally that will be just like your bike would have been now, thus making you whole. I.e. they are willing to replace the bike. Admittedly you lose a season of use that way, but that's difficult to value.
They attached a note saying that I can provide "comparables" - ads from people selling my bike in my area - to prove the value is higher.
You note that looking at current ads would value the bike less than what it was worth when it was in the accident. Have you considered looking for ads in print publications from the time of the accident? That should get around the things that you find unfair, as those would be ads in season, with similarly aged bikes, and better reflect the value of the bike then.
I'm more familiar with cars, which have things like Auto Trader which has local publications. I'm guessing that motorcycles have similar publications but don't know what they are.
Another option to consider is salvage. Do you concur that the bike is totaled? If not, take the salvage value off their offer and fix your original bike. I.e. they are offering $3500. When they total the bike, they sell it for salvage (or may pay to have it disposed of). Adjust the $3500 by that amount and say that you'll take that. They're happy with that amount and you have your bike back. If you can repair it within that, you're good to go.
Note that the bike may never run quite right. Perhaps it's not really straightened. Or something that you thought could be used can't. There is risk in this option, but it is an available option.
Of course, they may have already scrapped the bike, so this might not work. Or you might agree with them that the bike can't be fixed. I'm not saying that you should do this. I'm saying that it is possible to do this in some situations.
NADA has a glossary which says:
The base Manufacturers Suggested Retail Price at the time of introduction, including standard equipment only and excludes taxes, transportation and destination.
The MSRP should be the price at which the standard version of your bike sold when new. Your bike may have additional (non-standard) equipment plus other costs that would have increased that. You may want to document those extra costs.
I'm not familiar with Retail Clean, but the glossary suggests that Clean and Average are conditions of the bike. So Retail Clean would be the current retail price typical for that bike when in the Clean vehicle condition:
No mechanical defects and passes all necessary inspections with ease; paint, body and wheels may have minor surface scratching with a high gloss finish; interior reflects minimal soiling and wear, with all equipment in complete working order; vehicle has a clean title history; vehicle will need minimal reconditioning to be made ready for resale.
If this appears on the same page as the MSRP, I would assume that it regards the same package of bike. I.e. the standard options. If your bike had additional options, you will have to justify their valuation if you want them.
I continue to think that the easiest way to get full value is to look through print publications from the time of your accident for ads for equivalent bikes. That's their suggestion, so they should be willing to accept that information.
As a backup, you may want to try justifying the original price that you paid for the bike with the actual options. Then offer to accept 70% of that value. Why 70%? They offered $3500 based on an MSRP of $5000, which is 70%. The problem is that they may not be willing to assume that the discount is the same across all options. They may be more willing to embrace a comparables based argument.
In an ideal world, with infinite time, you might do both. But if you do just one, I'd concentrate on comparables.