Constantin,
I also tried the Bahbots bootloader and cores on a 1284. The bootloader installed correctly and programs would compile, but uploads would halt without an error message. My best results use a mix of brewtroller's bootloader/cores and Arduino-0022 cores. The procedure can be found in the last post of this thread. I've got no idea how this would affect your pin definitions, since my application was for a Sanguino.
Jon