In a medium bowl, shift together flour, baking soda, baking powder, salt, and cinnamon. Set aside.
In the bowl of a stand mixer fitted with the paddle attachment, combine butter and both sugars. Beat on medium speed until light and fluffy.
Reduce speed to low and add eggs and vanilla, beat until well combined. About 1-2 minutes.
Add flour and mix until mostly combined. Some flour streaks in dough are ok.
Add oatmeal, shredded coconut, toasted pecans, and 2 cups of the chopped chocolate. Mix on low until just combined being careful not to overmix dough. Overmixing the dough will result in dense cookies. Dough will be thick.
Cover with plastic wrap and refrigerate for 1 hour to overnight
Preheat oven to 350 degrees and line a baking sheet with parchment paper.
Scoop dough into balls (about 2 ½ tablespoons). If you have a food scale, dough should equal 1.7 ounces. Place 6 balls of dough onto the lined baking sheet, about two inches apart. Press 1/2 cup of chocolate chips into dough if desired.
Bake one sheet at a time for 9-12 minutes until the edges are golden brown (mine were done at 11 minutes). Cookies are better when they are slightly underbaked. They should look slightly gooey in the center and will harden as they cool.
Remove from the oven and let cookies sit on baking sheet for 3-5 minutes before transferring cookies to a wire rack to cool completely.
Store in an airtight container at room temperature for up to 5 days.