You can get hold of Pulse Ammo in two ways. Both will probably take some time though.

1. Fight enamies that drop or you can steal Energy Crystals from Like Behemoths, Ruby Dragons. Then use the AMMO REFINE ability to change them into Pulse Ammo.
2. Play cards and win Elnoyle Cards. You'll need 10 of them to make 1 Energy Crystal. Again use AMMO REFINE to make the Pulse Ammo.