How do you use the new items? (IE poison, etc)

They were disabled. They were only a proof-of-concept thing anyway. They may be accessible with quest rules or something sometime down the road.

Why?

Did they do the same thing as Din's fire? (I.E, replace the original items).

Yes. They were modified versions of existing items.

how about faroes wind and that other one??

Not implemented yet (even though in theory it should be rather simple to code, as all Farore's Wind has to do is modify the continue coordinates, and Nayru's Love would just negate the damage script).