Though I can honestly say that this is one of the games where stat-maxing is never gonna be needed, what I would suggest is that the first stat you max out is Yuffie's Luck. Start by giving her the following Materia setup:

Sneak Attack - Morph
Command Counter - Mime
Cover

It doesn't particularly matter if any of those are at master level or not: You're gonna get so much AP from doing this anyway.

Equip her with the Conformer; it doesn't matter what weapons and items you equip as they don't affect your actual stats, just seperate ones called Attack, Attack%, Defense, Defense% (Evasion), Magic Defense, Magic Defense% (Magic Evasion). Maxing out her Luck (I think it's Poodlers or Bad Raps; either way, the first hallway only ever pits you against those so you'll max out her Luck in no time) means that almost every hit with those Morphs she's gonna do will score critical, something which becomes essential once her level gets higher and the Conformer consequently gets ever so slightly weaker because your levels are now above those of the enemies.

I wouldn't recommend giving her the Mystile armlet as it gives you such a massive evasion boost which means she'll perform less Morphs by means of that Command Counter you've got.

Those six stats that can be augmented by Sources can go up to 255, although for some reason they may stop working when it reaches about 252 or 253. Don't ask me why, I just don't know :P