You mention a final certificate, who was this issued by, was it a QS or some other 3rd party, if so your initial move would be to query with them. Legally any dispute would probably be with them for an incorrect certificate rather than the builder.
The question of pay nothing until you have agreed the final amount, versus, pay what you think you owe and then argue about the rest is a tactical one. To be on the moral and legal high ground you should pay what you consider due and then argue the rest. However this is often a bad negotiating move.
You need to look at what the contract says about arbitration.
Note that arbitration is a highly defined process and not to be entered lightly. Mediation is a very different much more casual process if the contract allows should be considered before arbitration.
More info, amounts, who is certifying, nature of the dispute etc., would be needed for a fuller answer.