I can partially explain this to you, but, I do not know how you would go about getting the SFX numbers from Waluigi's AT form. Anyway, here's what the idea is here in PSA:
There's two SFX areas, you know how in most moves in other character's .PAC files there's "Low SFX: ###"? Well, that's generally one of two things, their voice they make when they do the move, or the move's SFX itself. Typically, the placement of the script for the SFX will tell you what it is but, it's wise to test what they are by deleting them and then trying the move in-game. How you would change those SFXs to Waluigi's would be to get the numbers used for Waluigi's AT and basically put in the #s for it in those SFX scripts in the .PAC for the moves you want them to be played for.
Easy, right? Yes. Well, the second area for SFX is the actual HITBOX SFX when the move actually hits a person. This is under the flags of the hitbox(es), I'm pretty sure it's the third from the last of the digits. AFAIK, the flags are in hex so you need to know the SFX # in hex to do this, they are two digits of course.
I'm sure someone can supply you with what each digit of the hitbox flags do. Anyway, there you would change the digits according to what you found from Waluigi's AT SFX. (I recommend talking to Kirk about this as he was able to get Captain Falcon to say "YES!" when the sweetspot of his knee hits someone).
In other words, it amounts to finding his SFX numbers and replacing the ones the Alloys use by typing in his numbers instead. Should work fine.