I have not done any Favors, so I do not know how they tie in with all of this.

2.0 nodes are basically 4 sets of one node each. Simply poking your nose into two sets after the first will cause the first to respawn.

3.0 nodes are basically 3 sets of two nodes each, and where applicable, a fourth set of 1 node, the Ephemeral Node. Just as with the 2.0 nodes, simply poking your nose in two sets after the first will cause the first to respawn.

I hope that clears up any confusion.