It's pretty ironic: for all the howling over shocked keys, shining scales and PVP trophies that went up when this crafting project was first released, I found that Flying Squid Ink ended up being the most obnoxious reagent to collect.
Farming Gannon's secret entrance is the way most of us have done it. The ink tends to drop about every 5 battles or so. If you time your farming efforts with a double reagent member benefit weekend, you can get two flying squid inks per battle instead of one. Even so, it's going to take a long time and lots of repeated battles.