I think this one will have to wait for Raze's expertise, as I don't have suggestions for how to fix it, but I'm a bit sad for you that you're running into multiple bugs.
Still, at least they're prepared to look into it, it seems.
As far as I remember, both of those things should just work, the nest towers should be fairly easily destroyed and with the possible exception of one area you should be able to transform back to a human whenever you want, even if it's not particularly advisable...
