Wanted to post the solution to the problem I was having, for anyone else who might have the same issue later.
Turns out, trying to compile the Arduino-usbdfu and Arduino-usbtoserial with an older GCC was a bad idea.
I built a new toolchain, using avr-libc 1.8.0 and avr-gcc 4.7.2, and using the simple combine script above, was able to get everything working fine.
Also, if you're on Mac, I put together a current toolchain builder, in case you don't want to wait for a CrossPack-AVR update. You can find it here: https://github.com/Pinoccio/pinoccio-firmware/blob/master/install-avr-gcc.sh
Thanks for everyone's help!