Again, I'd never heard of fate points until you mentioned them the other day. Belaboring the point that using them would have been helpful is meaningless, flogging a dead horse.
In answer to your question, the stun penalty no, the critical penalty yes. My GM said that the effects of the stun itself don't apply to trying to shake it off. (Thank goodness!)
That said, with 'only' a +29 stamina roll to start with (5 from faleeka, 4 from constitution, 20 from ranks in the stamina resistance skill), a -10 penalty from the critical (doubled to -20, courtesy of hollow bones), and a -10 penalty to resist the stun because hollow bones also extended the 1 round of stun into 2...
Well, let's just say resisting the stun would absolutely require getting over 95, and then not having bad luck on the second roll.
And by the way, you sound like you're a much nicer (or at least more competent) GM than mine. Still, the reason I was wearing soft leather is because I had weight other than my armor, like weapons, supplies, a frontpack (which is a backpack worn backwards... you know, because of the wings). And plus, I knew if we got any loot, I would have to carry some of it, and that potential weight loomed pretty heavily on my mind (and wings)!
*SIGH!* I didn't even live long enough to get any loot...