Yeah yeah I'll fix that.
Here's how I did it:
Take the 1024x1024 texture and divide it up into sixteen 256x256 textures. This is done easily in Photoshop by setting the square selection tool to a fixed size of 256x256. Setting the grid to line every 8 and 1 subdivision (or any power of 2) makes snapping the selection perfectly into place very easy.
Next, shrink each 256x256 texture to 254x254. Then enlarge the canvas to 256x256, leaving a white (or black or any color which easily contrasts your texture) border around the image. The width of the border is 1 px. You can easily automate this process with a simple Photoshop macro.
Now, go into JED and cleave the surface into 16 segments. Put the appropriate textures onto each surface and scale them to fit (fit WITH the border, as if it was a normal texture).
Now you have to change the UV coordinates so that the white border isn't visible. Do this by dividing 254 by 256 (254/256) and multiply that result by your current UV values. My UV values were 2, so I changed them to 1.984375, which is 254/256*2. Then you have to shift the textures around to make sure the white border isn't visible on any of the tiles. Normally, a shift value of 1 will shift a texture 1 pixel. Change it from 1 to 254/256 (0.9921875). Then shift the textures around until all the borders are gone. You may still see a few borders in JED, and you will certainly see them ingame, but we're about to fix that.
Now go back into Photoshop. We have to remove the white border, we'll do this by copying the edge pixels of the actual texture over the white border. So each edge will have two rows of duplicate pixels. This can also be automated with a simple macro.
Since the colors of the 1px borders are so similar, the hardware texture filtering used by JK will blend them together seamlessly.
Bassoon, n. A brazen instrument into which a fool blows out his brains.