[Ygorl]

The first gem raises the effective caster level for all purposes (right? certainly for purposes of if he or she can cast it at all...); additional gems reduce fatigue as you stated.

I don't know firsthand about the Army spells. I'm sure the protection stat increase (to 20?) doesn't stack (though the second one might boost it a bit more?) but I don't see any reason why you wouldn't get both the MR and FR bonuses...