I've never farmed before, so I'm unsure of how to do it. But from the looks of the script, it runs fert, then waits 31 minutes, does so again and runs a few other tasks. To accomplish these tasks you need to have the Action window open, the proper coordinates set, and be standing on your field.
After you go through the first set of instructions, you have it 'Exit farming Window to reset farming limit for next run'. I'm not sure where that mouse is clicking. Then you sleep for a server day, understandable, then click the sign next to your farm, why? This makes you run off the field and prevents you from doing any chores.
I used AutoIt's Window Info to get the coordinates and I believe they are set correctly, but I'm not sure I understand what the various MouseClick()'s are for. Can you explain?
Edit: Also, you mention you're running 2 clients, how does that work? You can only have one Mabinogi client open at a time as far as I know and I don't think you can log in under the same character. Unless you mean you have 2 different accounts running 2 different farms.