For whole grains bread, my machine has a 30 minute soak period before
it starts the mixing. Also, on of my books recommends soaking whole
wheat flour in some of the water before starting to mix whole wheat
bread.

Also, the bread rises more quickly with the addition of a small amount
of acid. I add a scant 1/4 tsp. of powdered lemon (unsweetened
Kool-Aid) to a 1 pound loaf.

Also, I add a tablespoon of vital gluten for each pound of bread that
is half whole wheat.

Just a few of ideas. But, I'm afraid bread with whole grains do not
rise a much as a high protein white flour, regardless of what is done.