David, whole grain baking is definitely a different "animal" and
using freshly ground whole grain flour is especially a different
animal. Try posting this in a group such as
<http://groups.yahoo.com/group/wholegrain-baking/>, where they
specialize in whole grain bread baking, including freshly milled
flour. Many folks there (especially Tom Park, a fresh milled whole
wheat expert) can help you for free!
A quick answer to your question: time. I've found that if you use
starters, poolishes and so on they break down the whole wheat enough
it can be become lighter. Also, you need to change your mixing
technique for fresh flour. (However, it will never be like a
pugliese or baguette so you do have to adjust your
expectations. Many people resort to the quick-n-dirty trick of
adding gluten (or white flour) to their whole grain breads to get the
rise up; I find that changes the taste so don't do it. Slashing and
shaping are pretty much the same with ww and white.