I honestly couldn't tell you basically anything about editing anything to do with the weapon graphic image file.
That said, I did miss the mention that you could see the palettes themselves but not the way they looked in GG - I didn't even consider that idea because I considered it fairly obvious, but I suppose you wouldn't have thought of poking around in GG since poking around in Shishi just made matters more confusing, not less, with its inability to display palettes 9-16 properly. Sort of not seeing the forest for the trees, which I did, too, by focusing on your mentions of trouble with Shishi itself.
Plus, doing this in GG would also require you to click a checkbox as you go or else it would be wildly inaccurate.
The image is only using the first palette - the first 16 colors. FFT imposes the next 16 colors, slot for slot, over the image when its palette is set to the next one. If you want to see what another palette looks like in practice, you need to import it overtop of the first palette. GG has an arrow near the colors, click it and you'll see options to Save/Load Palette or Color or whichever. Choose to Load the palette from the same file, turn OFF the checkbox option to Match Colors With Palette, drag over the 16 colors you want, and click them into place.
