Preheat oven to 400F°
Place cubed squash in a food processor and shred or finely dice
Melt ghee to large pan over medium heat
Add the diced squash and cook for about 10 minutes until it softens and begins to brown a little - stirring occasionally to move it around
While squash is cooking, peel and cut apple into four sections
Remove core from each piece and roughly chop into a few more pieces
Add to food processor and shred or dice apple
When squash is softened, add apple, spices, and honey to pan and stir to mix
Cook for another five minutes until apple is soften the mixture turns a deep golden brown
Remove from heat and stir in raisins
Allow to cool for 5 - 10 minutes
Move to a mixing bowl
Whisk eggs and coconut milk together
Stir in a third of the coconut milk until it is incorporated
Stir in the rest of the coconut milk
Place four ramekins into a larger baking dish
Divide mixture evenly among the ramekins
Drop chopped pecans over the tops of the mix in each ramekin
Dust with a little nutmeg
Pour cool water in larger baking dish so it surrounds the ramekins and comes up nearly halfway
Bake for 30 - 35 minutes until custard is set
Cool on wire rack for 10 minutes if serving warm
Cool completely on wire rack and then refrigerate for at least two hours if serving chilled