⭐ Merited by ETFbitcoin (1)
So I should do a transaction for each of the three main inputs to a different Ledger receive address (ignore the dust)?
That's what I would do 
The dust (0.00000546 BTC by any chance?) might have been part of a dust/spam-attack. If it's that small, it's not worth the transaction fee so don't add it. If it's more, you could add it together with the balance from the same address.