The icon support is very poor. I'm not filing a bug report as I see a problem in the concept. Please, add proper icon support, either ICNS that can locate and scale any size icon inside the ICNS (so that any standard ICNS will do, even with 16px icon scaled to 128px) or just drop support for that and replace it with support for transparent PNGs. That would simplify customization a lot - just replace a couple of standard PNGs with same size images and you're good to go.
I couldn't get the custom tool icons (func_x) work no matter what I did. The Leopard's Icon Composer didn't see any images within the original files so I wonder if they even are proper ICNS?! 48 pixels? There's no such default size in Icon Composer, only 512, 256, 128, 32 and 16! I DO have 128 pixel image and all the smaller ones but no, it doesn't work. My custom 128px OS icons that are made exactly in same way work fine so it's probably not about me doing something wrong.