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Sorry Jeff for the late response but I am new to the forums. I used to work for a company that are expert at moving data into and out of Intralink. I am still pretty tight with them. Let me know if it comes up again and I will put you in touch with them. They would basically "rent" you a tool to get your data out of Intralink and onto Windows in an organized format with XML files for structure and metadata. You would then have to write the code to move the files from Windows to PDMWE.
They have migrated tens of millions of files from Intralink to Windchill / PDMLink / Etc...