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In a medium bowl, whisk egg yolks into the milk, then set aside. Combine sugar and salt in a pan over medium-high heat. Slowly add milk mixture to the sugar, whisking constantly until the mixture comes to a low boil (takes about 10 minutes).
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Turn the heat down, and stir another 2 minutes, until mixture thickens. Remove from heat.
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Stir in butter, vanilla, and chocolate chips, mixing well until butter and chocolate is melted and incorporated. Transfer to a bowl, cover with plastic wrap, and refrigerate for 4-6 hours.
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Transfer cooled pudding into a large plastic bag, and cut off the corner. Gently squeeze the pudding mixture into the mason jars, on top of the graham cracker crust.