Update,
I pulled the brakes and all is as it should be. Put the bike on the center stand and spun the wheels. There is a slight rub but that is normal.
As far as Ethanol is concerned that has already been accounted for. I use to get 240 and tank, but once ethanol came to Kali it instantly dropped to 220-210 depending on the station. This has been a constant drop in mileage over the last month or so. Tank after tank I slowly got less and less.
To all, yes I never disconnected the O2 sensor. I just put the power commander to treat a severe case of throttle snatch. I knew that the PC reduced fuel economy, I just wanted to get a base line of what the bike was really getting to see if I just had a glitch. Turns out I got worse mileage without it.
For all those that question octane. I have two Volkswagens 1.8L turbos. They require 91 octane. I have put high octane in those cars for the last 10 years. They take 13 gallons a fill up. At this point paying what I pay for gas, adding an additional 5.5 gallons a week is a drop in the bucket. Besides, every time I have pulled the plugs they have looked perfect. With the questionable gas I get down here Ill stick to what works. Its just money, and for me a piece of mind. BTW I also pay $$$ for Yamalube 15w50 and a OEM filter every oil change.
I also pulled the oil filter while installing Brodies grounding harness. It still looked usable. Half was darker gray and the other half was normal gray. It will need changing during the next oil change, but light was coming through it so it wasnt overly dirty.
Funny thing. I wrote in one of my earlier posts that when the bike is cold and I let it warm up. Before I see any bars on the coolant gauge I would do a slow throttle roll and it would burp at 1500 rpm's. After installing the grounding harness I tried the same thing and didn't get the same results. I am going to ride the hell out of the bike this weekend and start a new test on Monday. I will post any results I get. Also I called my local Yamaha service center, Motoworld of El Cajon, and told them of my plight. The service manager, who has worked on my bike, told me he had another 06 FJR that was having the exact same issue. That bike was getting a new ECU. He told me to bring my bike in and they would check for the same issue. The only problem is they wouldnt get any new ECU's until August due to what is going on in Japan right now. Will also keep updated on this.