Well, I react pretty quickly with D to a food that causes me problems. Usually within the hour after eating it, it hits me. So I don't really need to do much trial-and-error to figure out my problem foods. I do make sure I eat completely safely all day except for that one possible problem food so I really know that was the only thing that could have affected me.
Sometimes I'll try a food on an empty stomach, and if I have D from that, I'll try it once more after a cushion of SF. It's not just about 'what you eat' but also 'how you eat it'. Especially for fruits and veggies I try to figure out how to eat them safely so that I can get the nutrients from them.
Did you eat anything else with the apple? And what did you eat the rest of the day, since you noticed the symptoms mainly at night.