I would assume whatever makes the most contact with the material you are mining, so for a hammer the head would make sense. Note: I haven't tested, it just makes sense to me.
Maybe it's one of those weird specialties. Like monastic requiring no entities nearby in order to produce mellow combs. Check your database and see if you can find if you're outside default territory.
Buildcraft pipes should take care of most of that. As for microblocks, I recall rumors of another mod that was similar, but I don't have a name for you, sorry.
You'll latch onto a few items that you always fall back to for certain aspects. Rubber = 2 impertio, 2 motus. Books for knowledge, of course, and so on.
I heard rumors that deleting the api in the buildcraft directory and restarting minecraft fixes this, but I haven't tested it myself, nor do I know what else that would do.