I can't resist reading your posts. They inspire me to try things I might not have done, and try to improve myself. Your enthusiasm is infectious!
The only thing I would say is be cautious with that first sharpening step. Sharpening is accumulative so if you go to heavy to start with, it limits what you can do later without causing unwanted artifacts.
As to the live view focus box, I just checked on my D7000 and the red box does not turn green when focus is achieved even when your not zoomed in. I assume it will probably be the same on the D90. But I don't see that as a drawback. With macro imaging the DOF is usually so narrow, especially with the lens wide open and the advantage of live view is not for a range finder, but to actually look at the focus achieved and place it precisely where you need to for your creative intent. That's where the zooming in really shines.