The game calculates PA/stone damage like this:
Say you're using Kraken's Spine.
With a 10 DPS Oilstone, it will add damage by multiplying 10 DPS by the relevant speed.
For autoattacks, this is 10*3.0
For abilities, this is 10*3.8
It then adds that number to the low and high end of the weapon.
For autoattacks, damage is now 166-283 every 3.0 seconds
For abilities, damage is 210-358