I think the MPEG streamclip option works fine, especially if you then copy your THM files into the folder that the new files are in and use the free version of QTChange (search for QTChange 0.7) to add timecode and reel numbers. The EOS plugin has me plenty of issues, and I'm not the only one who has run into them – I've spent plenty of time with other filmmakers in the Madison area trying to solve their issues with it.
You're definitely better off keeping your footage on an external FW800 drive (make sure the drive is 7200rpm not 5400) than on the internal. Also, backup, backup, backup. When that drive fails, what do you do?