One note to throw in re: target size:
You can print your own target from the included images that come with the software. If you have a very large printer (like the ubiquitous Pixma 100), you can print a really large one. There is a setting in the Focal preferences that allows you to measure the width of the target and input that, thus letting the software know what size target it's seeing and adjust accordingly. That has helped me a great deal while AFMA'ing on focal lengths of 400+ while still getting a decent distance to target.
Haven't tried manual myself, but I will next time. -tig