hi ^^
I love your mod, and I have a suggestion for you.
I don't know how it's made now, and if you can change it, but when you place a waystone, it is not active, right ? But it already have an identity.
It would be great if the waystone receive her identity when it is activated for the first time.
I suggest this, because i've tried to use a new waystone, in a "recurrent complex" structure, and the waystones are all the same, so it's useless..
In fact, I encounter the waystone, inactive, I touch it, and the next I encounter, is already active.

Sorry if my english is bad, I'm french =)

Not sure if it's going to work, but in the next version, in theory setting the name to %RANDOM% should cause it to not be generated until it's loaded the next time. So you would place it in the structure, enter %RANDOM% as name, save the structure, and hopefully all generated structures from that should receive a unique name.