If you have a lot of material to align, use it. It'll spare you an eternity. There is a reason why teams that build parallel corpora/megaTMs (europarl & acquis)
Basic workflow description:
you convert your files to txt,
run the europarl tool to chop it into sentences,
feed them to hunalign,
copy the output to excel,
delete unnecessary bits,
and insert tags to make a standard tmx file
(or wordfast translation memory) out of it,
copy to notepad, save and use in WF.
All of this can be automated; plustools for the txt conversion and command line for merging txt's, lots of search and replace and copy/paste all through.
Hunalign performs much better if you feed in a bilingual dictionary/glossary.
My workflow description:
I convert/save my files to/as txt,
sometimes Extract them into sentences with Wordfast/Tools/Extract,
feed them to hunalign = I use short editable bat file.
I open the output in MS Word (Excel cell has limited size), convert text to table and I delete 3rd column with index.
I break/split the table to 100-pages files.
I run PlusTools/+Align and open one short file with table created with PlusTools to activate +Align menu, I open file for correction and close short file.
I make corrections (mostly split some segment and delete tildas),
I create Wordfast TM with button Create TM. I merge all created TMs.
I tested Hunalign without the bilingual glossary only with "null.dic" on all EU languages in pairs with Czech.
I thank to authors of Hunalign for this free tool.
[Edited at 2008-07-24 19:09]