I created a portal and attempted to copy/paste it using WorldEdit, but when I paste the new portal it breaks and throws the invalid portal structure error. I can't get the pasted portal to work even if I remove some blocks and replace them.

WorldEdit isn't intended to work with any mods. Anything more complex than a decoration block can break when moved. I seriously doubt the dev will/can do anything about this.

That's unfortunate...Thanks!