Armor-Piercing Shot and armor mastery 2, 8 and 10

Armor-Piercing Shot and Armor-Piercing Strike both specifically reduce "DR from armor". They don’t "ignore armor". The effects of armor mastery 2, 8 and 10 apply in full against them.

Aim Tokens

Click on the link above to see errata and clarifications about Aim Tokens.

Using Weapons with the Thrown Descriptor in Melee

The Archer does not get his improved BAB when using a thrown weapon in melee. It’s a "Ranged Base Attack Bonus".

Storm of Arrows

Q: You can't do more than your Dex bonus in damage to an adjacent target. Do you have to allocate a seperate arrow for each point of damage? Say his Dex bonus was +4 and the target had four guys next to her, do you spend 8 tokens to get 16 extra arrows in the storm to hit all of them?

No. Additional targets suffer damage based on the total number of extra arrows fired, not the total number divided by the number of adjacent targets. In your example, 2 tokens to fire 4 arrows would be enough.

Q: Does DR apply against the damage?

Yes, DR applies.

Archers and Axe Mastery 3

See Axe Mastery in the Feats section for details.