clicking noises usually mean that you are printing too fast or not hot enough. Or there is too much friction in tghe filament feed setup.
It's basically cluicking because it can't feed the filament.
With the replicator clones it's usually because yoiu are trying to print too fast.
Great design machine - but fast it is not :-)

A hi-temp nozzle should work for all filaments. The only reason i can think of for them giving you 2 hotends is so you could have 2 different sized nozzles.

It always seemd a bit weird to me :-)