there are all kinds of things that can be done to change the tone.
how things are hooked up even the volume pot you use can play a part.
the wood body and neck play a part.
the finger board [maple or rose wood] both has a different sound.
there is a lot more then just the pickups or electronics wiring that make up good tone.
what kind of guitar are you trying to make and what is the sound your looking to get from this project. is the neck have a maple or rose wood finger board
will this be a hard tail body string through bridge
the more info you have the better reply you might get.