Just got your script yesterday. Been using it for a few hours testing the different settings. Just a couple notes I have seen:
1. When using the pre-walk method and the custom stack method (81-84) may I recommend that the script only pre-walk on the third (or final) deposit. Otherwise if the script pre-walks every time it looks rather bot-like. A human would see how much they have then go back to mining.
2. Repairing the wheel/hammer. May I recommend if this is checked it only repairs on the final stack (if doing more than one), this also makes it look like a bot. Nobody would repair it then go back to mining (and not drop the hammer either). They would repair it after their sack is full (unless they can't deposit).
3. The walking method to the stairs and to the sack. Always clicking the map then the respective object is a bit bot-like as well. Always walking to the same spot, and not an efficient area either (west of the sack or east of the stairs).
4. Finally, I would recommend if gathering gems, you add the option to bank them after depositing the minerals in the hopper. This way, they can gather 28 on the next trip. Rather than ending with 3 or 4 gems by the final deposit and having to do a 4th trip.
Besides those few notes I find your script absolutely beautiful.