By "pbboom" he means "prboom", which is a Doom engine/port.
You won't be able to really change the banner and icon with just the CIA (well, you probably could by extracting them and then replacing them with ctrtool and stuff, but why go to the trouble? The source for Doom is readily available). I suggest compiling it from source code and replacing the banner.bin and icon.bin yourself.
I compiled it anyway (including support for N3DS buttons, 804mhz, and L2 cache, but it should work fine on old 3DS too), so here it is.