Use Common sense. Which FDA and health dept seems to be short on. HACCP is a joke and the records can be easily manipulated. Which they are quite regularly. The best advice: Do not sell a product that you would not eat yourself.
I had a rule for all my cooks, that I learned from my mentor early in my chef career. He would say "If my family, or my grandma walked through the door right now, would you feed it to them/her?"
Unfortunately, you have to follow all health dept regulations, even those that are over kill or wrong. I remember having a fruit fly problem on onions, so we built an outdoor storage shed and stored the onions in there. It was a battle, and my argument was, once I brought the onions in he would write me up for a fly problem, which he agreed, but he wrote me up for outdoor storage, and the only solution was to process the onions when they arrived and store them in the walk-in.
Honesty and integrity are key. My family actually asked me on Sunday how many times I fed food that fell on the floor. I could honestly tell them that I fired every cook that tried to serve it, because I could walk up to any table and say "Hey, your food on the floor. Instead of serving it to you, we are comping it and remaking it." No one ever complained.
Do what's right and the rest will fall into place. And work with the health dept, and treat them like partners. I know I complain about them a lot because we had our issues, but I always maintained the attitude of partners and never feared them.