This doesn't sound good.
Which dealer? Have they contacted Yamaha? Have you considered calling Yamaha Customer Service?
You will have to work on understanding that you are a 1/10-percenter. Many of us have tens of thousands of miles on our bikes with none of the issues you are reporting so it's difficult for us to "walk in your shoes".
Your report indicates they've changed the TPS...IIRC, that isn't required on the '09, only the older iterations. Arriving at 32 days in the shop might be close to the lemon-law in CA. You'd need to check and not take my word for it.
I am truly sorry to hear of your problems. Believe me when I say yours is a rare experience. Not to say this is the bike for everyone, it's not, and over the years a few have admitted so and gone elsewhere in the Sport Touring spectrum.
It sounds more to me that your dealer is incapable of diagnosing and repairing your motorcycle, hence my second question at beginning of my response.
My first FJR came with Bridgestones (it was totaled on Hwy 49), my second came with Metzlers. I wasn't happy with either so I changed them at the first opportunity. YMMV....tires are far too personal a subject.
My windshield has never "squeeked" though the rubber seal the "U" bracket slides through will occasionally rub against the metal. My bags don't rattle, there are adjustments for the bags (the lower mounts come with shims and the dealer should know that).
It really sounds to me that your dealer is letting you down. That's a shame. I
ll be crossing my fingers for you.
M