I'm sorry you're having trouble, Chloe. I'm just guessing at this point, but not taking throttle points to dirty carbs.
Revving up and down on her own at 60 mph could be dirty carbs surging, or a cylinder intermittently losing spark. When I got my 250 used, its carbs were dirty and I had noticeable surging at 55 mph. I assume when you said "revving up and down" you meant that you could feel the bike speeding up and slowing down on its own, as in surging.
The clunkiness at idle sounds like the typical clutch noise that old 250s develop. Does it get better if you pull in the clutch lever? It could also be cam chain noise.
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