I used to do something similar with PDFs, using one of two methods.
1) Oscar's File Renamer Free
This is an extremely unusual file renamer that makes the list of file names to be changed text-editable. That is, it's more like using a text editor. Changes are not committed until you press the Go button, so you can finally exit Acrobat or whatever viewer after your last file, then rename the files in one go. It works well, but I found the interface a bit strange, and went on to a simpler means (2, below). Oscar's is now available in original Free version, which has some problems on Vista or Win7, as noted on his Web site, plus a Pro version that fixes them and adds an improved scripting feature. Pro is an "Unlimited Evaluation Version" with a nag screen. $15 removes the nag.
2) Make a directory list, usually by a plugin for Total Commander, or by redirecting dir/b into a file in a DOS box. Edit the list into a batch file, something liketemp.bat
ren "010339.pdf" "@@@.pdf"
ren "ningauble 072.pdf" "@@@.pdf"
ren "0946_sheelba.pdf" "@@@.pdf"
where the "@@@" are placeholders for the new names. Alt-Tab between the viewer, accumulate the text you need, Alt-Tab back to the editor, reformat your text as necessary, and insert it into the "@@@". When you've finished your list of files, exit your reader and run temp.bat. Without paths, it obviously has to be in the same directory as the files to be renamed.