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Good luck with your project. Looks promising.
You wrote: "Wondering if the nitrites that showed up on day 2 are from incomplete nitrification, or coming from manure that's part of the organic compost. Should I wait it out to see if it comes down or change out the water?"

The nitrites probably came from the soil. (There's plenty of nitrification going on in bagged soils before they are ever put into the tank.) I would change the water for sure.
 

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I hope your plants are growing. That's critical to bringing the ammonia and nitrites down.
Aquarium test kits measure NH3 plus NH4+
I would use your own judgement on when to do a water change.
 
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