Pre-soaking and boiling of wood (and changing the tannin stained water regularly) will help to remove most of their tannins which lower pH, but generally most wood will still continue releasing tannins even after being pre-soaked, just at a lower rate, hence there will still be some pH reducing effect over time.
pH of 6.0 is okay for plants, the lower pH is mostly likely from the combination of wood pieces and the bacteria activity from processing the bio-load waste. Your fishes will be fine in that pH too.
For sand substrate tanks, you may need to adjust the fert dosing abit more (but not too much until algae take over) as there is no active soil substrate to gradually release nutrients. Your plants could also just be adapting to the new tank conditions so it might take some time for them to transition, since they are mostly slow growing plants anyways.
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