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Being I didn't understand 99% of your post, a couple of observations..
I don't think I've ever heard of the factory CO settings BOTH being set at 0.
Both, from what I've read both here and on the FJR forum, CO #'s are always set on the positive side and are rarely at the same setting (as you noted, the inner cylinders running slightly higher). The FJR having FOUR separate TB's, has 4 separate CO settings, again, all almost always being different from each other.
The TPS can be set for a slightly higher # if running lean (per Mama Yamaha in Ca, on my FJR while at the shop-running issues)
Randy, with the ignition was advanced, did you notice the lope happen to increase after that or when?
Perhaps returning the timing back to stock, the base air screw to 3/4 (page 3-7) turns out and bumping the CO settings (going to have to guestamate there, 5-25 or so?) and then go from there..
I don't think I've ever heard of the factory CO settings BOTH being set at 0.
Both, from what I've read both here and on the FJR forum, CO #'s are always set on the positive side and are rarely at the same setting (as you noted, the inner cylinders running slightly higher). The FJR having FOUR separate TB's, has 4 separate CO settings, again, all almost always being different from each other.
The TPS can be set for a slightly higher # if running lean (per Mama Yamaha in Ca, on my FJR while at the shop-running issues)
Randy, with the ignition was advanced, did you notice the lope happen to increase after that or when?
Perhaps returning the timing back to stock, the base air screw to 3/4 (page 3-7) turns out and bumping the CO settings (going to have to guestamate there, 5-25 or so?) and then go from there..