hey jbuy41, i had some problems too to use correctly the focus stacking in the past. After reading well the guides and try by myself i found a workflow that works very well, and it's esay to use (for me).
1. activate the follow focus from the focus magic lantern menu
2. switch the liveview on
3. now you have live view with the FF++ FF-- on the screen. Now you go to the focus you want to use to start (you can go manually, or with autofocus, or using the arrow keys (up a down go fast, left and right more precise adjustments).
4. When you are on the starting focus point for you stack, return in the magic lantern menu, and go to focus end point, and press set.
5. now you are again in live view and should have something like: Focus End Point: 0, not configured
6. use the main wheel (not the one on the back, but the one you use for the shutter time, the one near to the shutte button. If you turn clockwise the focus point go near you, if counterclockwise the focus goes far from you (i use always this, because i set first the nearest point of focus, but it can works in all the 2 ways).
7. when you turn the wheel you can see the on screen text changing, and saying the number of steps between the start point and where you are (for example it says: Focus End Point: +18 steps from here)
8. When arrived on the last point of focus, go again in the ml menu, go to rack focus, and then press "set" (i don't know if this part is really needed for focus stacking, but is useful to see if the range is correct, because the focus returns from the last point to the first that you have selected in point 4.
9. when the rack focus is finished and you are again in the starting point, simply go again in ml menu, set Stack focus to snap and then you are ready for taking the shots. You take the first, and magic lanter do the rest.
Hope it helps, anyway i've wrote a tutorial about focus stacking using magic lantern, but because i'm italian and my english is not so clear, at this time my tutorial is in the hands of Bart, that will correct and structure it, and hope soon you can see it in this site, as an article or something like this
