I just can not figure out how to change the perk to remove the "if not wearing armor" requirement. Anyone know how to do it? Some help would be much appreciated.

The conditions are placed on the spell concerned rather than the perk.

If you look at the Stoneflesh Spell, and bring up the effects list (Right click, edit). You will see 4 Effects, open up any of the effects associated with the perk, and you will see the conditions which have to be met for the perk to be applied, 2 of the conditions relate to wearing armour.