The problem is that I will need to modify the bootloader to use it properly.
Also, I want to make the name "Protoduino"... Is this copyrighted, or is it available?
Before I start that, how thick is thr Arduino coating?As in, how drastic is the change from Arduino to that AVR thing?
In case you missed it, the common part of these tasks is the "Figure out on your own", where - in case you missed that again - the important part is "on your own" and not by posting questions on the forums. This will teach you a lot of useful things, most of them you probably don't even know yet that you need them and it will set you on track for you little project.