Novamanga, I took my own crack at fixing the texture pack the other day. After hours of trial and error, I managed to fix all but a couple of "block" textures.
- The security manager I couldn't begin to think of how to save without actually using a texture editor.
- The constructor/destructor/detector/reader all have the same texture. I'm honestly not sure if that's how it's supposed to be or not, as I've never used any of those 4 items.
Finally, some of the blocks have lost their "glow" effect, while others (like all the different grids) managed to keep it.
In order for some of the repairs to work, the side texture of the fluid grid and a couple others to be a flat panel like the other blocks.
It appears you've fixed the processors and other items; I didn't look at that or the gui folder.
So, I highly suggest you to compare my patch to yours and take anything that you need.
That said, I'm pleasantly surprised with how well the repair job went.

I've never made a texture-pack texture before and did nothing but cut/paste and rename blocks. This is entirely a workaround/jerry-rig until someone simply edits the textures, as it's not a perfect patch.
As an added bonus, I've included a patch for the "Refined Storage Addons" mod inside as well. That mod only adds 1 item to the game, the "wireless crafting grid". I used the same texture the "wireless crafting monitor" in Refined Storage. It would be very considerate if you added that mod into this mod's patch for sake of convenience.