You did everything I would have done.
I have 4 Media100 systems. So I have a little experience with Media100 problems. And believe me when i say there have been numerous issues.
Once I had horrible problems similar to yours but my files were relatively small. We were producing TV commercials primarily. I had a bad cable going to my external RAID. It took me forever to figure out what was going on. Go figure. When external drives start going bad, it can be a nightmare. Don’t be so quick to blame the Media100. Look at everything and I mean everything.
The idea that the fellow had about breaking your project into smaller pieces and then combining later on into a final larger project sounds like how I might have approached such an enormous project.
I’ve done 2 hour projects off my 8.2.2 system and not missed a beat, but I am operating off a gigabit ethernet server running on 4 – 250gig drives operating on Windows NT. (I guess Windows OS is good for something?) I definately think out of the box.
Good luck.