Gap Insurance is a coverage that will pay the difference between what your regular insurance will pay for a totaled or stolen, etc. bike and what you owe on the bike at the time you put in the claim. Say your insurance will give you $3,500 on a claim for a totaled bike and you owe $4,200, then the Gap Ins. will pay the $700 difference.
Some lenders will require you get Gap Ins. if you don't have much of a credit history or your FICO credit score is below a certain number. Yamaha dealers use Synchrony Bank a lot for customer financing. I think they may have a deal going with them.
Gap Ins. isn't usually regarded as necessary for a purchase as low as the R3s price OTD.
Extended Warranties give you Peace Of Mind in case anything breaks on the bike after the factory warranty runs out at 12 months. My experience is that modern bikes don't break, so I never buy extended warranties. IF you were using the bike as a commuter and put a LOT of miles on it per year (like 10K or more per year), you MIGHT want to get the extended warranty.
You can still negotiate the OTD price. This time of year, as we get closer to End of Motorcycling Season, dealers will start reducing the prices on their R3s and MAY lower or drop any Freight & Setup charges they have been adding throughout the Summer. It's worth trying to the charges dropped on both the bike cost and any dealer add-ons. You can usually get a discount on any accessories and gear that you buy at the same time as the bike, too. 15% is usually the maximum discount offered on accessories, but on gear it can be as much as 50%, depending on the dealership. Sales are slowing down in most areas of the country ( sales may not slow down until November in warmer areas) and dealers don't want to have to pay "Flooring Fees" to their lender on unsold bikes, so they try to get them out the door, even it means they just break even on the deal.
Your finance % rate will be based on your credit score. That wouldn't be negotiable since it's set by the lender.
If you live somewhere near a Costco, call them and see if they have a buying plan set up with any local dealership(s). This is usually the easiest way to buy. The price is already fixed, no haggling, and is usually a good deal.
You just join COSTCO for $50, they give you a Gift Card back for $25-$50 and tell you who to see at the dealership. Some Forum members have gotten REALLY good prices this way. Put COSTCO in the Forum search box to find them.
Alternately, you can just call each dealership and ask for an OTD price from a salesman. DEFINITELY let them know you are shopping around for the best price and make sure they give you the TOTAL OTD price.
Hope this helps some.....