The tannins/staining is going to point at the dirted sub as the culprit. You could try a bag of Purigen in your filter to remove the staining and organics, but you'll have to keep it replenished over the next year either by cleaning the Purigen with bleach, or just replacing it every so often.
If your heart is set on tear down and rebuild - Malaysian trumpets are pretty hardy. Toss some cucumber into the tank, or something else that they'll flock to and munch on and then just grab a hand full of them. You only need a few, and they'll breed back up to whatever quantity the tank can sustain in no time based on food availability.
My tank journal.
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