Had the same problem with a large XML file the other day.
The solution I went for was to split up the document (in Notepad or XML-Editor), but this, of course, means that you have to be familiar with manipulating source Xml code.
Disappointing Trados behaviour - mind you, WinAlign had problems aligning a - perfectly edited XML-file - 100000W file. I spilt it up in three parts and it worked, so in your case you may need to split up your doc in ca. 20 smaller files (35000W/file) - good luck.
Just suggesting: what happens, if you align the corresponding ttx -files?
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