For a cast iron closet/toilet flange, should the Johnny bolts used to attach the toilet to the flange be made of brass or stainless steel or other? If brass, will it eventually corrode the cast iron closet/toilet flange?

Yes, that should be brass: 5/16" x 3 1/2". No, they will not corrode. If too long, cut them of with hack saw after toilet is installed.