Prepare a work surface by laying out two 3-feet long pieces of parchment paper, overlapping slightly.
After popping the popcorn, transfer it to a bowl. Lift the popcorn with your hands and shake the bowl lightly so the unpopped kernels fall to the bottom. Lift the 4 quarts of popcorn out of the bowl and transfer to a large brown paper grocery bag. (I like to place the grocery bag on a clean towel in my sink. This is a better height than on the countertop to pour in the caramel sauce.)
Combine the butter, brown sugars, corn syrup, maple syrup, molasses and salt in a large microwave-safe bowl. Place in the microwave and heat on high power for 2 minutes. Stir to combine. If the butter is not completely melted, return to the microwave for another 30-60 seconds.
After stirring, return to the microwave for 1 minute. The mixture should be bubbling up furiously by this point. Remove bowl and stir well then return to the microwave for another minute. Repeat this cooking and stirring for a total of 3 minutes.
Remove the bowl from the microwave and stir in the vanilla and baking soda. Stir well until all of the baking soda is well incorporated. Add the pecans and stir for 30 seconds to ensure that the pecans are well coated with the caramel.
Pour the hot mixture right into the center of the popcorn in the bag. Fold the top of the bag down once and shake, shake, shake to distribute syrup through the corn.
Microwave on high power for 1 minute. Remove the bag and hold it at the top and one of the bottom corners. Shake well the return to the microwave for another minute. Repeat cooking and shaking two more times for a total of 4 minutes. Turn the popcorn out onto the prepared parchment paper. Sprinkle with flaky sea salt, if desired. Allow to cool completely.
Store in an airtight container. The caramel corn will keep well for 1-2 weeks.