Preheat oven to 400°F.
Roast halved squash for about 45 minutes, or until they are spoon-soft. (Alternatively, you may pierce with a fork and microwave until soft.)
Scoop out squash flesh – measure 1 1/2 cups into a large bowl. Mash eggs, water, oil, and sugars into the squash.
Whisk flours, baking powder, baking soda, and spices together, and then mix into the squash mixture.
Fold in raisins.
Spoon batter into paper-lined or oil-sprayed muffin tins – half to 2/3 full.
Bake in pre-heated oven until muffins test done with a toothpick – about 15 minutes. Cool in pans for 10 minutes before removing to cool further.
Serving Size muffins