Align two PDFs files using Trados WinAlign

I need to align two PDFs files using Trados WinAlign. The deliverable will be a translation memory ideally in Trados Studio 2009 format. The original PDFs files have 400 pages (each one, the target and the source) almost 150.000 words and have a complex format with plenty of number tables. The source language is English and the target language is Spanish. They are Clinical Trials. The documents are ok in terms of translation and the only work needed is to confirm the correct segments are accurately aligned. Some PDFs manipulation experience may be needed.