Not too sure what software you're using to do your wireframes, but
I've designed and specified websites before with a similar sort of
complexity using Axure. Axure allowed me to create wireframes with
different panels in the page and different states for each panel.
Axure has a great prototyping feature and also the ability to export
specifications to a Word document. When exporting, all of the
features, panels and states are automatically described in the
specifications document. Therefore if you update your wireframes, you
simply re generate the specs. I understand that it's difficult to
switch software half way through wireframing, but I'd recommend you
take a look perhaps for next time.