I have a few questions.. and may have some time to think about this..
Do you have door locks controlled by the Elk, or just sensors?
How would you activate these modes? (function key, task, etc.)
How many extra modes would you need to support?
With what you've described so far, you could use tasks, perhaps mapped to function keys, that armed the system, set an output to flag the mode, bypassed the appropriate sensors, and disabled the appropriate locks. Then, if you wanted to do something when it was disarmed, you have the output set when the system is disarmed, so you can call the cell, flash the siren, etc.. when your wife disarms the system. Please let me know what's not acceptable with this solution.