Job is done and paid in full and remaining payment was matched but I can't seem to be able to match the three email transfers that were sent as a deposit for the job.

I'm assuming you used the 'Receive Payments' function to record your deposits prior to the job being done.  When you receive a payment without linking it to a particular invoice, QBO saves it as a credit to your customer.

Once your invoice is created, go back to the payment you received for that customer, and a list of outstanding invoices will be shown.  Apply the credit to the applicable invoice(s) and save.  This is probably easiest done by going to Sales-->Customers and viewing the Transaction List.  You will see any unapplied credits there.  Open them and apply the payments to the outstanding transaction(s).