Thanks SkyWalker9,
It looks like the "Add a set_aflock 1 to the start of the script ..." might be what I'm looking for.
Nope that didn't work either.
Weird... if I set MF distance to hyperfocal distance (based on f /stop and zoom focal-length) then shoot by pressing the shutter button the exif data shows the subject distance of 1.6. Then if I set the focus to hyperfocal distance and run an intervalometer script the subject distance listed in the exif data shows 64.4 (same as infinity). There is a very noticeable difference in the sharpness of the images. The hyperfocal distance being superior.
I went back and looked in the manual and it said "Remember to exit <ALT> mode to shoot pictures with these adjustments applied."