How long does it take for vitamins to get out of your system like iron, zinc or D3 that you take daily?

Quite variable. Only one of the things you mentioned, d3, is a vitamin; the others are minerals. B vitamins and vit. C are water-soluble; other than B12 they are not stored in your system and leave within several hours. The fat-soluble vitamins a, d, e & k can stay for several weeks, as can minerals- for example iron can be stored for several months.