If the son has paid some of his father’s mortgage liabilities, surely, that is a debt of the father’s estate now due to the son. It is therefore important that it is not dressed up as a legacy.
To my mind, it would seem sufficient merely to include within the clause directing payment of debts, funeral expenses, etc., to specifically identify that the debts include the sums paid by the son.
It would probably be helpful to prepare an acknowledgement identifying the current indebtedness and for the father to acknowledge the indebtedness on a regular basis, say once every 5 years, to avoid any arguments over the possibility of the debt becoming stature barred. Such acknowledgement might include an update, if appropriate of the amount of the debt outstanding.
If the above were to be adopted and the son die before his father, the debt would be an assets of the son’s estate, and would remain payable on the father’s death.