There's a lot of stuff to change for ammo:
Throughout items.qc are things like bound_other_ammo, the ammo item spawn functions, etc.
weapons.qc uses ammo when firing its guns and for determining which gun you can use.
client.qc spawns you with certain amounts of each ammo.
It's a good idea to do a text search through each of these files for the word ammo. Don't change anything yet, just browse around and see the places it's used.