Thats a sign its lean. Give the gas in the tank (that has Seafoam in it) time to work. It will start cleaning itself if its a gunked up gas issue. I think you said earlier the previous owner had screwed up the jets by drilling them, if thats the case, you may have put in to small of jets. Double check the needle height, some bikes it is adjustable. For a lean high speed issue, you would RAISE the needle, in other words, LOWER the clip.
Since you found the rubber boots not on the carbs correctaly, that is a suspected air leak spot and could be causing the lean problems. You may need to replace them because if they were put on folded or funky, they might not ever go back to shape. Test like other engines by using a propane torch to look for leaks or using grease to do a temp air seal.
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You said it, tank vent. Usually in the gas cap. Rust or bugs plugged it up. A plugged vent could be your lean issue as well as the other problems I listed. Its an easy test too, open the gas cap and do it redneck style, put a yellow chore glove in the tank to keep the gas from slopping out and take a ride. Smile at the people laughing at you....
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