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I get black smoke and kind of a fluttering, belching no idle situation till it sorts itself out.
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Black smoke indicates that the engine is running rich (too much fuel).
If this were mine (the tractor), I would do (or have done) a good & complete tune up, Carb cleaned, rebuilt, and adjusted. Regardless of the PTO situation, this needs to be done.
Your situation sounds like it has multiple issues, nothing major, but you have to tackle these issue(s) one at a time.