Assuming I am understanding what you are asking for, this is how I would do it.
Step 1: Establishing what your power source is.
As I see it this is best done with aspects. First have your High Concept be something like Auto-Biomancer (meaning essentially that you are a specialized practitioner who uses body-altering magic on yourself). Go ahead and throw something like My Powers are Magic! somewhere on your aspect list to reinforce that. Or don't, if you are pressed for aspects, you really said it all in your High Concept already.
Step 2: Choosing your Powers
I'm going to take what you mentioned earlier: Enhancements for your strength, hardiness, speed, and perception.
For speed we are choosing Inhuman Speed [-2] and for strength we have Inhuman Strength [-2], easy enough. For perception let's choose Supernatural Sense [-1] which lets you see in the dark, echolocate, smell algebra, or whatever you choose as a super-sense, go nuts. That leaves us with Hardiness, which we will simulate with Inhuman Toughness [-2]. Now all toughness powers need what is called a Catch, which means that they need some kryptonite factor that will pierce them. Let's deal with that in step 3.
Step 3: Choose your limitations
We already know we need a catch for your toughness power, so lets choose that first. The Catch can be anything from silver to sunlight and holy water to whatever else you can think of. It gives you a refund of +0 to +4 of the refresh that you spent back, depending on how obvious the weakness is and how easy it is to find. For you we only want a refund of +1, since you can't get more back from the Catch than you spent on Toughness in the first place. I'm going to say that your rocky skin helps to turn aside blades and energy, but not blunt force, which can still shock your bones and internal organs on impact, thus giving your Toughness the Catch Blunt Trauma. It's not obvious because you look so impervious, but is very easy to find, giving it the refund value of +1.
Now we're not done yet, because there is another refund you can take advantage of. Because you must invoke your powers with a transformation, we are taking the Shapechange ability Human Form, which states that your supernatural abilities are unavailable so long as you appear human. When you do access them, you physically change in obvious and threatening ways; your skin takes on the appearance of rock, your eyes and mouth leak fire, and thundercracks accompany the movement of your magically accelerated limbs. Because this leaves you pretty defenseless so long as your abilities aren't activated, it is worth the refund of +1.
Step 4: Add everything up
And this is what your final powers list looks like:
Human Form [+1] attached to
Inhuman Speed [-2]
Inhuman Strength [-2]
Supernatural Sense [-1]
Inhuman Toughness [2]
The Catch [+1] is blunt trauma.
Total refresh spent: -5
So that handily comes in at just under the lowest refresh level stated in the book, feet in the water. And don't let the fact that you chose the bottom level for your speed, toughness, and strength abilities fool you; you will be a beast in combat. Hope that helps!
