I'm 6-0", with a 34" inseam (High Pockets PANTS). This is my 2nd FJR, and I put 60,000 miles on the first one.
1. I'd start with something non-ergonomic - electrical. Think about what 12V accessories you will want and get them now. Here's why - without a doubt, my biggest PITA with my first bike was dealing with electrical gremlins associated with my 12V accessory farkles. I bought them one at a time and ended up with this ridiculous rats nest wiring harness that was both an embarrassment and a curse. Purchase a FZ-1 Fuse Block and mount it under the rider's seat. The FZ-1 is a great F/B because it comes with a heavy duty relay and you can switch each circuit from "always on" to "ignition on" and visa versa simply by just moving the fuse. You can pick up a relay trigger source of power from the license plate light wire right next to where you will be mounting the F/B. Then I'd run ONE set of wires from the battery, and build my custom wiring loom to include ALL of my accessories at once - shrink wrap and tie wrap everything super water tight using HIGH QUALITY connectors. That's what I'd do.... wait a minute, that's exactly what I did!!! You can read about it in a thread entitled "Farkling Pants".
2. Opinions on windscreens are like pie holes and crap holes... everybody's got one. This much I know - a barn door won't work at high speed (80 mph +) on the slab in DIRTY AIR - getting around a lot of 18-wheelers in a high cross wind, for example. However, for 99% of all conditions, the Cee Bailey Sport seems to work well. Yesterday, on a desolate section of the slab in clean conditions, I ran the cruise control up to 102 (max speed setting) and held it there for 2-4 miles. I could have held it there all day. Rock solid. The tinted screen look bad-ass too.
3. If you are going to ride more than 100 miles in any given day, then you really should treat yourself to an aftermarket seat. Russel Day Long wants to build a customized tractor seat that COMPLETELY covers every square millimeter of your tushy. He will adjust the seat location front or back a smidge to suite your leg and arm length. Then he wants to put you in that extremely comfortable lazy boy and YOU CANNOT MOVE.
Seth Laam has a different perspective. He will build you a customized semi-tractor seat that will allow the distribution of your arse-load, but not quite as much as RDL. As a trade off, if you desire, you get to move a little in the twisties, shifting your weight back and forth.
I don't know much about the other seat guys. If you are not planning to ever ride more than 100 miles in a day, then the FJR is not really the bike for you. Go ahead and trade it on a sport bike or a pirate ship.
3. It's a 600 pound bike dry, and it ridden like it's meant to, will be loaded with 75-200 more pounds of gas, crap and peeps, not counting yourself. The likelihood of a tip-over is pretty good. Frame sliders, at minimum, are really a must.
4. If you are planning to install a top box, there have been an incidence of the stock rear rack (plastic) failing. There have also been a lesser incidence of the rear frame cracking - both issues are from the high load of a top box. At a minimum, the Givi SR-357 rear rack will do a much better job of distributing the load. Another option is to purchase the "Stiffy Kit" from forum member Garauld, who ingeniously designed a channel-section-based way to greatly stiffen the rear frame without any cutting or welding.
I think the Givi V-46 top box strikes a nice compromise between looks and cargo carrying capability.
5. I'd hold off on bar risers until you ride the bike a while, and make a decision regarding your seat. I moved the bars to the rear setting and it was close for me. Then after the Seth Laam seat, it's really nice. I had 1" heli-bar risers on my Gen 1 bike, but don't need them for this one.
Hope this helps and I hope you enjoy your new FJR. Welcome to the madness!!!!