Ive completely rescaped tanks, including new substrate and planting with fish in before. Just be careful how you do it.
Just rinse off anything in water, doesnt really matter if its tank water or tap water.
Be aware that any new wood will float for several weeks or maybe even months and leach tannins. You can presoak before putting into your tank until it gets fully waterlogged, or weigh it down. Boiling the wood can also help, its a good practice to boil wood anyway, although ive never bothered and never had an issue.