Do old and new item bonuses stack?
I can now confirm that not only do they NOT stack, but also that only the bonus from your old boots will take effect!
It seems that the bonus effect from Kanai Cube will be disabled if you also have the same item equipped on your body. So in your case, you will only have 100% damage increase (not 350% or 450%) if you equip those old boots!
So if want the 350% damage increase, you cannot equip the old boots on your character.
Source: http://us.battle.net/forums/en/d3/topic/20749236496