Well, you don't give alot of info here especially regarding things like your location, riding skill level, expectations for the bike or its intended use for you, but I can touch on a few basics.
If you plan on riding in any kind of inclement weather, the V-Strom handguards just might be the best bang-for-the-buck add-on you could purchase for your FJR, IMHO. If you're in cooler climes, a set of grip heaters are nice as well, although I'm personally a big fan of the cheaper alternatives, rather than the oh-so-pricey factory jobs. If you think you're going to want a top case on your feej, you'd be crazy to let your old one go with the old bike, unless it's in rough shape. It won't add much to your resale value, and then you'll just have to pay a bigger price to get another one. I do believe the side cases will hold an XL FF helmet, but what if you've already got other stuff in them, or have more than just a helmet to stow? Myself, like many others here have come up with other alternatives for helmet stowage. Lots of good tank bags out there if you need the extra space, I have two myself for my FJR...a small sport pack and a big mother, both magnetic and both expandable, so I'm pretty well covered there. Some form of throttle lock or cruise control are a must if you plan on doing any serious mileage. Windshields and seats are sooooooo subjective, but I think most will agree that the stockers are underwhelming at best. And remember that changing either will affect the other, so the smart thing to do (although not necessarily the easiest to accomplish), is to find other owners in your area who might be willing to let you throw a leg over or maybe even put a few miles on their particular setup. Otherwise it's a crap-shoot. I've lost count of how many different windshields I've tried now.
I think those are the basics. Beyond that, the sky and your wallet are the limits. It will likely be long time before you run out of things you can buy for this bike.
Good luck with your forthcoming acquisition.
