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If dirt in fact slipped past the air filter, I’d expect to see some inside the intake.
I am a little suspect that the bike didn’t need a top end:
-bike suddenly runs rough at 6k miles
-top end done: bike still runs rough $2,000
-fuel filter and seals replaced: bike runs great
Maybe the top end had plenty of life left in it, and it just needed a new fuel filter and seal kit?
Yeah, I am salty.
It’s been Hard for me to get momentum of enjoyment for these Husky/KTM bikes. Even people with the same bike seem to have it easier.