You asked :" Are his allowances for 2013/14 9940 been used against the pension first? "
It depends what his tax code is for his pension, and whether his pension income is above or below the personal allowance. If his pension exceeds the personal allowance then he will taxed at basic rate on his new job. If his pension income is less than his personal allowance then he will be due a rebate at the end of each tax year and should consider asking for his tax code to be split between jobs or applied to the new job if that salary is more than his pension