I am making a bible cake.  Should I use fondant or gum-paste to make the rosary.  How should I still the beads together

If the cross and beads are sitting on top of the Bible, then fondant would be fine.  If you are having them "cascade" down (ie half on half off) the Bible, then use gumpaste for its extra stability/strength so they don't crack on transport.

I would use a (silicon) pearl string mould to make the beads (then they are already stuck together in one long piece). 

i would use fondant plus cornstarch kneaded in to strengthen it so they could be pleasantly eaten -- also might add some raspberry flavor oil

For flowers I would prefer the gum paste. For the bible and the cross I would use fondant.

I usually use gumpaste. Wilton has a mold that has the pearl beads. I would use that.