Update as of yesterday:
Worked 8 days in a row, finally had yesterday off. Broke out the dial indicator again and looked over everything better when I wasn't so tired. The Rim itself runs with 0 runout measured on the abs ring lip on the wheel (rotor side) with the ring removed and on the shaft drive side on the hub of the wheel. So that eliminates the wheel bearings/bent axel/etc. I still had 15 thousandths runout on the rotor face, clearly something is wrong. I pulled the rotor off and measured each of the surfaces the rotor bolts to on the wheel. The runout was 7 to 10 thousandths between sides. So the wheel itself is not machined properly, which causes the rotor to not run true when its bolted tight to the wheel. Now the factory rotor had no shims on it, and I wondered how it could have run true at anypoint considering the wheel wasn't machined properly. Well I put it on a granite table top and used a dial indicator to check measurements. I found out that the tabs of the rotor that bolt to the wheel were actually not completely flat, all of them were bent inward toward the wheel mounting side and some were worse than others. After some tinkering, I found out that if the factory rotor is positioned in one position on the wheel, will run with around a 6 thousandths runout vs 15+. I have formed a logical idea as to the big picture of what happened. The wheel was off spec, the brake rotor ran true. The brake rotor was "bent" at the factory to run true to my particular wheel. Due to usage over 12K miles the rear rotor on my bike started to warp back straight, which caused the grinding noise I heard before I swapped tires/rear brake pads (the noise that I thought was from the brake pads being shot). That noise was due to the rotor being 6-7thousandths runout and coming in contact with the brake caliper bracket that doesn't move.
I have started to come up with a plan since I refuse to spend the crazy money on a new wheel through the dealer and I can't locate a used one yet at this point. I made my own shims and managed to shim the backside of the new rotor between the rotor and hub, and get the total runout down to under 2 thousandths. The rotor runs very close to true now, but the rotor itself is still too close to the brake caliper bracket and rubs it. I already filed the opening on the caliper bracket a bit which helped, but it still needs more. My only option at this point is to possibly machine down the aluminum axel spacer between the wheel bearing and the caliper bracket, about 6 thousandths should give me perfect clearance on the rotor to caliper bracket. I don't think that small of a decrease in width will cause a issue with swingarm as the axel nut is tightened.
When it comes down to it I will still likely buy a replacement wheel for my bike since mine isn't machined properly and it will likely cause future issues with my bike. I am going to be sending pics and runout measurements to triumph to see what they have to say. I doubt they will do anything about it but its worth it to see what happens. I will keep youguys posted.
EDIT: I have no idea how triumph machines the wheels. I asumme they are casted, and then chucked in a CNC lathe that machines the faces. Well my wheel must have been chucked in the lathe crooked, which it why both the lip of the rim and the mounting surfaces where the brake rotor bolt to show excessive runout. Bummer really..
