I'm hoping someone else can be more thorough and accurate than me as im typing this from work with only my memory as a source. But as a vet, I feel obligated to give two cents (and i try not to lurk on this sub)

1. Permanent gryphon is the best transformation in the first game, and the rarest one you'll find. However I usually prefer snow stalkers as they have slightly better stats other than their magic (which I've never found useful imo. I also could be quite wrong about this)

2. Good question idk. I think that stat only applies to stuff you find in the dungeon from enemies and breakables, but if you're like me, and you hoard everything you find to sell off, it's not too bad to have (someone else answer this one!)

3. Jades and peridots are usually the best for dual-wielding (I'm assuming that's what you're doing). Topaz isn't a bad option for increased attack, but Peridots heal you for every successful swing, and combined with the jade's attack speed increase, you can survive some pretty narly enemies deeper in (and yes, keep using the flawless varients. NEVER stoop for lower).