Modifying wiring for one sketch

My question is:

Can I make a sketch use a modified version of wiring.h and all the related files, with the modified version only used in that sketch? In other words, can I cancel the inclusion of the original wiring.h and substitute my own file?

One of my intents with this is to modify the timer code that uses timer0 for millis(), etc. Just as an extra timer for a project.


Just write the new initialization and setup of the timer in the setup() and its done.