Bitcoins exist as 'unspent transaction outputs' (UTXOs), not as an 'address with a balance'. If you really feel the need, you could import your keys into some wallet software which will allow you to exercise 'coin control', which means you will be able to pick and choose which UTXOs are used as inputs when creating a transaction. So then you could just choose all your UTXOs and send them to a new address in a single transaction, and then do the same for your wife's UTXOs.
But doing so will put your funds at additional risk, as you'll have to trust the new wallet software/device you import your wallet into. Mishandling private keys can lead to a loss of funds (theft), so you shouldn't do this unless you feel it is absolutely necessary.
Really, I would just create a transaction that pays you your share of the coins, and another transaction paying the remaining coins to your wife. Within a bitcoin transaction, it does not make any sense to point to some specific output and say "these bitcoins came from this specific input". Rather, it is as if all of the input coins are melted down into one blob, and then the output coins are forged anew from this blob. So it doesn't make too much sense to worry about tracking 'your specific coins' through time, as each 'specific coin' is 'melted down' when it is used as input to a transaction.
Think about it like this: when you do your accounting, do you worry about the serial numbers printed on the $20 bills, or the value of them? Your bitcoin accounting can work in much the same way: how much bitcoin did you buy? How much did you sell? This is the relevant information.
Will this work and be cool to the ATO?
Questions about how to satiate the demands of any particular tax authority are going to be off-topic here, you'd do better asking an accountant or tax lawyer if you need such advice.