Search for pp_substr in pp.c.
It's not a good idea to want to modify substr on that level. You can use subs (I think) and override substr with your own custom function. That makes it still a bad idea, but at least you can write your replacement in Perl that way.
What problem are you trying to solve that involves replacing substr?
Update: subs seems to be the wrong module, but I'm sure I remember a module that allowed one to replace built-ins. Maybe I'm just thinking of CORE::GLOBAL:: though:
BEGIN{
*CORE::GLOBAL::substr=sub($$$) { die };
}
print substr 'foo',2,3;
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