Sorry to hear you are having the problems with the FJR. I just passed 600 miles on my 06 FJR. I changed the oil and filter at 200 miles. In addition, I recently added Shell Rotella T synthetic motor oil and Mobil 1 gear oil at 600 miles. Boy, she is silky smooth now. I was fairly aggressive during break in too. I rode it hard, but no red line and no extended revs.
Here's some of the complaints I've read about and my experience so far:
1. Heat - I'm getting some heat on my left leg when temps are greater than 80 degrees. Not a big deal and I don't plan on any mods to correct this.
2. Surging - I'm coming from a modified Bandit 1200S so the surging issue is a non-starter for me. From a dead stop, I need to be a little careful, but I've already adjusted to it. I won't be taking any tension springs out of the throttle either.
3. Handling - This bike handles really well at moderate to high speeds, better than my Bandit. I love weaving through traffic with the torque and handling combo this bike offers. You have to be aware tooling around at slow speeds as this is a big bike.
4. Wind protection - Coming from a Bandit, the wind protection on the FJR is pristine. I think the stock shield is okay, but I am ordering a CalSci +2.5 windshield to hopefully get a calm air pocket with the shield fully extended for the long trips.
5. Seat - The seat is not as comfortable for me, 5'9", 190lbs. I am going to ride the stocker this year to see if I adapt to it. Otherwise, I'll see if the wife lets me splurg for a Corbin.
6. Power - Well documented. It's there. There is a reason that Yamaha recommends experienced riders for this bike.
7. Brakes - I love the linked brakes. For the ultra experienced riders, this may be a turn off, but it works well for me.
8. Other issues - My MPG is stuck at 17 like all the early production bikes. Not a big deal. I'm sure there will be a fix for this.
The drain plug for gear oil was pretty loose. I thought this was double checked at the factory.
My dealer found crate damage on the lower right side fairing. The dealer ordered a new part and charged Yamaha. I also discovered after taking the bike home that my dealer broke an allen wrench part inside one of the allens at the bottom of the W on the windshield. When I pick up my lower fairing part, I'll have the dealer check this out too and make necessary repairs.
Overall - The bike delivers the goods. It's a perfect bike for my needs. I look forward to many miles and years of enjoyment. I highly recommend this bike.