I am unsure if you are able to use other codecs but you can use the lagarith codec (google it) to preserve transparancy or uncompressed avi if either of those are available.
If not, download the trial of Vegas pro8 and finish your project there- just remember you can't open the saved file in Vegas Studio (the project file).
Not sure about Vegas Studio and kinda going from memory here but in Vegas Pro I believe if you render as an AVI uncompressed you will have transparency if when you bring it into a project, you right click the clip on the timeline, go to Properties, and on the Media tab change the Alpha Channel to "Straight (unmatted).
You might want to test this on a small clip, I'd hate for you to spend 8 hours rendering only to find out I was wrong!
Lagarith preserves transparency? Are you sure? I've never tried it, but I've always been under the impression that it was Uncompressed or bust. (Or Quicktime.)
Can't try it right now -- I'm on my notebook which, for some reason, doesn't seem to have Lagarith installed.
So far, a Quicktime video format with PNG compression is the best I've found that will preserve the alpha layer. Quality is the same as uncompressed and the file size is smaller than Lagarith. If anyone knows an even better alpha layer format, please tell us. For now though, as far as I know Quicktime PNG is it.