Scoring Idea

[angrave]

Every click costs a point or more (including line swaps and the play button)
You start with 100+x points where x is the minimum points required to complete the level.

[Swotfabs]

In theory this could be done by manually adding up the minimum required for each level, and then having the swap button, delete button, and insertCommand buttons decrease this number.
That said, the largest thing holding this back right now are the not-very-well-known ace editor keyboard shortcuts.
As it stands, you can use alt-upArrow and alt-downArrow to swap a line up or down (which is really useful when you are using a device which doesn't have a touch screen).
The problem with the keyboard shortcuts right now is that they ignore prefix and suffix length and will let you swap everything.
Ace allows one to create custom keyboard shortcuts which is what we will have to do if we want to have the keyboard shortcuts also decrease the score, and not mess with the prefix/suffix text.