If it is untyped (as is the case with Giant Form) then yes, it should stack.
Yes, but remember that you take an AC penalty for size. Table 8-1 [CRB179] details the penalties. But I will repeat them here for ease of use:
Colossal -8
Gargantuan -4
Huge -2
Large -1
Medium 0
Small +1
Tiny +2
Diminutive +4
Fine +8
Yes.
A natural armor bonus improves Armor Class resulting from a creature's naturally tough hide. Natural armor bonuses stack with all other bonuses to Armor Class (even with armor bonuses) except other natural armor bonuses. Some magical effects (such as the barkskin spell) grant an enhancement bonus to the creature's existing natural armor bonus, which has the effect of increasing the natural armor's overall bonus to Armor Class. A natural armor bonus doesn't apply against touch attacks.
So you have a base "Natural Armor bonus" and can have one "enchantment bonus to existing Natural Armor bonus". All creatures are said to have at least a +0 NA Bonus.
The distinction is important. A troglodyte (+6 NA Bonus) that uses Giant Shape 1 now has a +4 NA Bonus. Not +6 or +10, as the Giant Shape 1 replaced the Trog's inherent NA Bonus.
If it is untyped (as is the case with Giant Form) then yes, it should stack.
You're right for the wrong reason, heh. Natural Armor is called a Bonus for some reason (a hold over from other D&D editions and because it is a bonus to your AC). It isn't a "typed" or "untyped" bonus. It simply is the number that goes in the NA Bonus box when adding things up.
There is also the "Enchantment Bonus to Natural Armor Bonus" box that is a typed bonus. It is a bonus for the NA bonus and you can only have one enchantment of NA.
So a creature with +6 NA bonus and a +4 barkskin and a +2 amulet of natural armor has a +10 to AC. If the Trog uses Giant Shape 1, it'll drop down to +4 NA +4 barkskin = +8 to AC.