Sorry for my delay in following through on a focus stacking forkflow. I moved and have just started school, so I’ve been very busy!
First, I’ll start with an example image that is a stack made of 12 images. Each image was manually focused using high magnification live view, and I still made mistakes in focusing too far between frames. “Over focusing” results in the strange areas of blurriness that you see when zoomed in to the full resolution. Some are indicated using black arrows, but there are still other areas blurred in just this small crop. So, the lesson to take from this exercise is that you should try and remove human error at every point possible