Trying to do deep focus photography with a long lens is not recommended, as the number of focus brackets will be high.
Trying to offset the number of brackets by shutting down the aperture will not help that much, because of the increase in diffraction.
Thus deep focus photography is well suited to wide angle lenses that are not stopped down too much, ie by 2-3 stops from their widest aperture is a sweet spot.
When auto bracketing on my 5D3 I tend to use my 12-24mm Sigma.
To illustrate why 24mm is the widest I would go, consider the use case: the minimum focus distance of the Sigma is 280mm. The maximum magnification at the 24mm end is 0.17. If I use an aperture of, say, f/7.1, this will result in around 16 brackets from 280mm focus to my infinity focus at 3 x hyperfocal, using my current bracketing algorithm. I set the bracket to bracket overlap at 30 microns.
To further illustrate why you need this large number of brackets I've created a lo-fi video of how Helicon Focus stacks these 16 images. In this video you get a real impression of the limited depth of focus for each bracket.
I'll keep refining the script, because it's fun for me to do. For instance it's now at release 1.65 ;)