Oh, nothing of that nature. The "surround coding", if you will, is based on the phase of the sound wave. It would take a pretty determined effort to screw up the audio - though I, for one, find the audio mix to be fine (my 5.1 soundtrack simply steered the various tracks to their respective speakers, though I did have to lower the volume on the rear channels.)
"In AE (as of right now) I plan on replacing the captured little black bars with 1-color black boxes to help the bit-rate issues they present."
Unnecessary. Simply crop them out from your initial video capture. The black bars have to be there in the final product in order to make a "legal" frame size, but your mastering program should be able to put them in for you. Anything you add on top of this would unnecessarily add to the overall bitrate. I used to do this in Vegas before I learned how to crop the files in Virtualdub. It will also reduce the filesize of your masters and AVIs.
"I'll output a monster interlaced 29.97 fps video.
This raw video will probably be 1 gig per minute if it is a lossless QT video using the component codec."
Actually, it'll be a monster 23.976+2-3 pulldown monster.
(If you convert a 24fps directly to 29fps, you get stuttering video). It would be interesting to see how big your video ultimately is, since laserman and I both came up with 200GB captures with uncompressed RGB."Their compression scheme for lossless is awesome. This will allow me to easily archive all of my footage. Each movie should end up being roughly 60 gigs in the media 100 format. The downside to this is that this footage will require their card to be edited in the future."
That's about what I get with HuffyUV (actually, a bit less.)
"If I need to use some of the filtering you guys are using to remove halo/ghosting etc can those filters be ran on QT files?"
I'm unsure if AVISynth will work on QT files. Are you going to transcode your Media 100 files into QT/AVI files (and keeping the masters as M100)?