I'm not sure about the studs fitting under the caps, though I'd like to know myself (maybe I'll pick up a set for street duty). The lug nuts -- you will definitely need open ended. That could be stock but if you have exposed lug rims you will most likely need different ones.
I have seen ARP or Moser studs on a car with ponies before, and no, he couldn't put the center caps on because they did not fit with the long studs. I didn't know some were "thread in" or "bolt in".. new to me, but granted... I've never installed aftermarket axles.
Ive never heard of a c clip breaking. What usually happens is that the axle itself will break. So no matter what the c-clip is made of, it aint gonna hold thte axle from sliding out. Thats why you should switch to eliminators or 9" ends if you plan on running in the 11s