Bo, If you want it all dug out, now is the time to get that done. The footer and stem wall would be poured before the concrete floor in most cases, but that varies by region I have learned here. In the mid-South it seems common to pour the floor and use it as a foundation for the stem wall. Did you pass on the full basement thought?
In terms of your log laying schedule, the stem wall should have some time to harden up before you do any heavy work on or around it. Maybe a concrete person will chime in on how long that could take. They are fragile for a while.
EDIT: I noticed your footer trenches were dug out precisely and cleaned up real square, which probably means the contractor isn't planning on using any form boards for the footer pour. If you have it all dug out, that will change his plans, but not a biggie at this point I think.