This recipe was inspired by Chris Kimball's Milk Street recipe which calls for 1 cup of rye flour which you toast in a skillet. This is a less intensely rye version with only ½ cup of toasted rye and a different mixing method. Makes about 26 oz of dough, 36 with chips and 40 oz with nuts.
Preheat the oven to 350 degrees with the rack in the middle position. Line 1 baking sheet with parchment. This is so you can bake some test cookies, but plan on (also) doing this later in the process because these cookies are the best with dough that's been chilled for 24 hours.
In a large skillet, toast the 1 cup of rye flour (or half rye and half ap) by heating over medium and moving it around with heavy duty scraper until it starts to darken a little and become fragrant. Scrape it into a bowl and let it cool slightly. It will have lost some moisture and should be around 125 grams now. If it's very lumpy, you can sift it.
Add 1 cup (125 grams) of all purpose flour, baking soda and salt and whisk to remove lumps.
Brown the 12 tablespoons of salted butter. Once brown and fragrant, add vanilla bean paste and molasses and let cool.
In a stand mixer bowl fitted with the whisk attachment, beat the eggs and sugar for at least 3 minutes or until thick light in color. Turn down the mixer to medium and stream in the melted butter (or do it by hand with a whisk).
Remove the mixer from the stand and stir in the flour mixture by hand using a heavy duty scraper. If you'd rather use the mixer for this, switch to the paddle attachment and use low speed of the mixer. The dough should be soft and almost candy-like and probably a little warm if your butter wasn't completely cool. Let it stand for 10 minutes, then stir in the chocolate chips.
Use a medium size scoop and scoop out balls of dough and put most of them on dinner plates lined with plastic wrap. Cover with plastic wrap and forget about them for a day or two. Meanwhile, bake up some immediate gratification cookies.
Arrange on parchment lined baking sheet, spacing 2 inches apart. Sprinkle sea salt over cookies (if you like) and bake for about 8-12 minutes, rotating the sheet halfway through.
Immediately remove parchment paper from tray and let cookies cool on parchment on the counter for about 10 minutes, then transfer to a rack or a plate and let cool completely.
Notes
If using unsalted, you might want to increase the salt to 1 teaspoon.