What non-daily dungeon awards the highest Gil/Stamina?
For now you should just focus on picking and choosing what you upgrade. Eventually you will run into an event that will make you several millions of Gil. Until then, your best bet is just grinding the Gil daily. There really isn't many stages that are great for getting gold.
Your FF VI: Mobliz Elite is likely the best for now. I can't confirm since I haven't done an exhaustive search, but typically I don't seem to find much Gil in standard Stages.