Check the floatheight, it the fuellevel is too low, the bike will starve for gas at higher speeds. Had this exact problem on a friends xt550. Also check the filter under the floatvalve.
I wouldnt mess with jetting, all my tests have shown that theese bikes are slightly too rich at the mainjets, even with a higher flowing exhaust and modified air intake/filters. This is backup up by dyno runs and my of test with air/fuel tests with a lambda prope in the header on my exhaust. I've never experienced the stuff JJ writes,but have heard about it with pod filters mounted directly on the carb. So I guess theres a lot of variantions to consider.
Oil in the airbox is often becasue the bike is overfilled with oil.
I can highly recommend this supercheap carb rebuild kit: https://www.ebay.com/itm/Yamaha-Carb...from=R40&rt=nc
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