I have been experimenting with photo stacking for some time using the free software 'CombineZP' but only recently have I played about with changing the point of focus.
Here are some of my experiments using a couple of timber and ore wagons
Using a Canon 350D, first I used the manual point of focus setting for the following shots. They were then stacked using CombineZP.
Unfortunately there are only 5 manual focus points on the horizontal plane (there are only 3 in the vertical plane) and for some reason I cannot seem to select the one on the extreme left (unless it is selected but the LED has died). This means that some of it is out of focus.
The last photo is taken using the cameras Auto Depth of field function and then 6 shots stacked.
It has turned out to be the best of all of them.