Oleg, 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.
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