In a medium saucepan over medium heat, add the split vanilla bean, cinnamon and nutmeg. Bring the milk to just a simmer, cover and turn off the heat. Let the spices steep, about 15 minutes.
In a large nonreactive bowl, add the egg yolks and both sugars. Whisk until the sugar is mostly dissolved into the egg yolks, about 2 minutes.
Temper the eggs into the milk by adding 1 cup or so cooled milk to the egg mixture, whisking constantly. Continue slowly adding the milk to the egg mixture until both are combined.
Transfer the milk mixture back to the saucepan and cook over low heat, stirring constantly with a wooden spoon, until the mixture is thick enough to coat back of the spoon, 2 minutes or so. Remove the pan from the heat and add the heavy cream, vanilla extract and salt. Strain through a fine sieve into a cooled bowl. Stir the mixture occasionally until cooled completely. Stir the vanilla extract into the cooled custard. Refrigerate for 1 hour.
Pour the mixture into an ice cream maker and freeze according to the manufacturers' instructions. Serve the ice cream in waffle cones and garnish with chopped Marcona almonds and coarse sea salt.