I went back to attempting the macrophotography project I had tried starting last Thursday. I realized the problem I was having was that I had been trying to figure out how to mount my camera on the micrometer stage, when I should be mounting my subject on the stage.
For a first shot, I wanted something simple, with lots of texture and a bit of color. Last night we popped some popcorn to have with a movie, so I grabbed a left-over piece and put it on the stage. Here's a shot of the popcorn that I got when it first came into focus. Notice that the bottom of the kernel is more in focus than the top.
With the stage I can move the kernel by tiny steps and bring it into the focal plane of the camera. The next shot is an image from the middle of the sequence of images that I took. Over all, the focus is better than the first shot, but there are still places on the kernel that aren't quite in focus.
I found a piece of software that I'm trying out which aligns and stacks all the images in a sequence to make the entire subject come into focus. I'm pleased with the result for my first try, but I think I overdid the color correction. Something weird happened with the black background which makes it look more grainy and less black.