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The factory pilots are slightly lean, but the mains are on the rich side to avoid toasting the engine at big throttle settings. The shims are probably not necessary. If the air filter has only 500 miles and the problem started about 500 miles ago... You see where I'm going with this right? It's probably over-oiled. If it's like mine, it just needs a mist of oil on the furry side. It does not need to be saturated.
Could be a mouse nest in the air box too. I had one of those in my Concours airbox once and it ran horribly.