In my own experience it does take a few days for the phe levels to come down. The important thing is that your son's phe levels are coming down. Continue doing what you are doing and if for some reason your sons phe levels stop decreasing his doctors will need to decrease the amount of regular baby formula he is drinking and increase his PKU formula.
Please let me know if there is anyway I can help. Your son will be just fine, and like I said it does take a short while to get the phe levels down to an acceptable range.