Ahh, the joys of new FJR ownership. Kinda makes me warm and fuzzy inside.
I'm going on 5 years now on my 03 purchased Fall of 02. That's a record for me, usually after 2 years I want something else. But, no the FJR is a keeper.
Granted, yes, you do have to tweak it a little to suite your individual riding style and personal preference. But that's prettyy common on any bike, me thinks.
Some advice for you:
1.) Loosen the main throttle spring, get BMW touring grips, heavier bar ends, and do the throttle body sync. It will be much smoother, I promise!!!! Oh, and the engine naturally smooths out over the first few thousand miles.
2.) Windshields. Interesting topic, a lot of advice will be given if you ask. My 03 has a different front fairing design, so I can't say it you'll have the same experience, but it should be fairly close, so here goes. The stock one just sucked, period. I'm 6'2" and wanted a quiet bubble to ride in. I first tried the Rifle Touring w/ tuning block. Nice, but not perfect! Looking for something better, I tried a Cee Baileys +4. Also nice, but too short for me so I sold it (probably would be ideal for 5'8"ish). I also did not like the distorted bend in the shield. Went back to Rifle touring for a couple of years, then tried the monster x-tall CalSci shield this spring.
https://motorcycleinfo.calsci.com/FJR1300.html
This is the shitz!!!! Much quieter, smoother than anything I've tried. GET THIS ONE!!!!!!!!!
3.) Knee pain. Try the Wild Bill highway pegs (if he even makes them for an 07, I frankly do not know). Changing positions helps stretch out a little when you need it. Also stand up once in awhile. Also, I started drinking Mona-vie, one of these high anti-oxidant, glucosomine suppliment fruit drinks. Wow, no more knee popping or joint pain. It also just generally makes you feel more energized. I just got back from a 2600 mile trip without any knee pain at all (granted I have highway pegs) I'm a distributor if you want to try a sample for a few weeks.
4.) Consider the different bar adjustments you have available stock, experiment and see if you need some other solution. Yes, your bike has factory adjustable bars!
5.) Evaluate your helmet for noise and WEAR EAR PLUGS! I had a Nolan for years and thought it was a good helmet. Then got a Shoei Syncrotec and realized just how much of a POS the Nolan was.
Other little goodies like Grip puppies are an excellent idea. I personally don't feel the need with proper tuneup, heavy bar ends and BMW grips, but can see why others love 'em.
All of these items should be fairly cheap, except the shield is pricey, but worth every cent you'll pay and should last for many years.
Hmmm...that should do it for now. You may also want to consider a throttle lock (the el-cheapo Vista cruise works really well, IMO).
Then the real farkling will begin. Trunk, lights, suspension upgrades, elec cruise, heated stuff, etc....all will provide more comfort and allow you to go longer distances in comfort.
Enjoy the new bike and welcome to the dark side!!!!!!!!!!!!!!!