As soon as you've finished loading (skip the story sequence by pressing ESC), use your Stone of Instant Transmission (don't worry, it doesn't get used up).

Remember, you need to use the Stone of Instant Transmission before you "Break Rock" or it won't work.

The Stone of Instant Transmission will take you to the Sub-boss area. Break all three pillars (left/right, top has to be last). Focus on the Spirit Tree as it's the only one you have to kill to move on.

Beat the boss as quickly as possible and warp back to the square. At the square you can turn in your quest and get a SCM. Get the quest again and repeat as many times as you like.
The Fast Exit

If you want to farm even faster you can use the Fast Exit trick to skip the scoring and rewards screens.

To Fast Exit, you need to pop up the "Menu" and select "Select Square". You should be doing this during the boss loading screen.

If there are other players you need to select Go Separately (or do a Group Fast Exit, not explained here). When the square select screen pops up, click one of the squares but don't double click a square or press connect yet.

Now you need to fight the boss. All your controls still work while the square select screen is up, it's just a bit distracting visually.

When the boss is about to die get Lunia Gold your hand ready on the mouse. As soon as you see it die press connect as fast as you can. Just as the stage clear is starting to appear the loading screen will show up and you'll be taken to the square.
Summery and Speed Tips

- Get/use the Stone of Instant Transmission.
- Wait till you're level 35+ to do scm runs.
- Use Tia as she is the fastest runner in the square.
- Break all three pillars at once.
- Target the Spirit Tree, it's the only one you need to beat to move on.
- Start the Fast Exit while the "Boss" is being displayed.
- Finish Fast Exit exactly after you kill the boss.