The type of flour that you use will have a profound effect on the outcome. Since my recipes work well with the type of flour that I use, I thought it would be of value to talk about what I'm using. If you're using a different type of whole wheat flour, your results may differ, or you may want to slightly alter the amount of liquid you use.
The flour that I use in my recipes is whole grain whole wheat bread flour. I buy it through a third party seller, but I get 10 lb. bags that are shipped from the mill and obviously intended for more commercial rather than personal use. I buy my flour this way because it is much cheaper than buying small bags at Japanese supermarkets and I use a lot of flour. The value of using this type of flour is that it keeps the nutritional benefits intact, is unbleached, and as high protein as possible. The appearance is of relatively larger grains that are light brown in color.
Because I use this type of flour, rather than more finely ground or bleached "white" whole wheat flour, I have to give it a little extra time to absorb moisture. This is why my baking recipes recommend allowing the batter to rest for 15-30 minutes. The flour being more fully hydrated will allow for a better rise and texture in the final product. I don't recommend using specialty whole wheat flour such as that which is ground more finely for baking because it removes some of the wheat germ and you lose the benefits of the whole grain and some of the protein. However, you can use any type of whole wheat flour that you like and adjust the resting time (or eliminate it) to your particular flour.
In general, the finer the flour, the less of a need there is for resting the batter and possibly the less moisture you will need. The only way to know for sure is to experiment with your particular type of flour. If your baked goods are too dense, doughy, or dry and the baking time in your experience seems very different from that recommended in the recipe, then you may need to adjust the amount of liquid (usually low-fat milk) or applesauce a little to improve the texture and bring your result more in line with mine.
In general in regards to the batter type:
Fruit- or vegetable-based cakes or muffins:
The batter should be relatively thick to provide structure and accommodate the extra moisture from the fruit or vegetables. The batter generally needs to be spooned into the baking pans.
Flavored cakes or muffins (e.g., chocolate):
The batter should resemble thick cake batter. It should be pourable, but spooning it is possible as well.
Since whole wheat flour is richer in gluten than white flour, it's even more important not to overwork it when you mix the batter. One of the reasons why I always say to stir only until moistened prior to mixing in the baking powder is that stirring too much will work the gluten (the protein in wheat flour) and make tough baked goods. When you're working with whole wheat (and especially with quick breads or thicker batters), always mix as little as possible while still making sure all ingredients are adequately incorporated.
If you have any problems with the results of my recipes, I welcome questions and will be happy to try and help you get a better result.
One of the things most people aren't aware of is that baking is chemistry. :-) Glad to see you are aware of that and know how to adjust your recipes to make sure things work correctly.
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