To help answer this, it's important to know that there are two formulas needed to calculate your total damage. The first one is used to calculate the weapons damage, which

**only** uses any enhanced damage or +max/min damage on the weapon itself (I won't list it here, as knowing it won't help your question).

The second formula is performed after the first, and is used to calcuate your total damage. This formula is:

Min Damage: [Weapon Min Damage + (+min damage)] * (1 + Stat Damage Multiplier + ED%/100)

Max Damage: [Weapon Max Damage + (+max damage)] * (1 + Stat Damage Multiplier + ED%/100)

The "Weapon Min Damage" and "Weapon Max Damage" are the values worked out in the first formula. The ED% (and the +min/max) in this one takes into account any enhanced damage from items other than the weapon itself. You'll also notice the stat damage multiplier is in this formula as well, which is where the strength multiplier would come into effect.

So, to answer your question, the enhanced damage from a fortitude armor is applied after calculating the weapons damage, and is applied at the same time as the strength modifier.

Chilling armor seems to be applied onto your total defence. In other words, after your total armor defence is calculated (including the 200% on the runeword, though possibly excluding skill defences, like Shout or Defiance).

Having found not much on penetrate around, I can only really take a logical guess at this. Penetrate is calculate first, because when you put a point into it, it takes up your attack rating permanently. I believe it applies the % AR bonus to your "base" attack rating (excluding any AR you get from skills, such as Jab). The new attack rating you have after putting a point into penetrate becomes your new "base" attack rating.

The attack rating bonus given by Jab is applied to your "base" AR when determing the chance you have to hit with that skill. I believe it's applied after taking into account the bonus given by penetrate. I'm sure someone will correct me if I'm wrong