Wow... sounds like this is a touchy subject for ya...
This page doesn't get as much traffic as, say, the 7.3 general fourum... try posting this there, you'll likely get more responce...
I am, for sure, not up to giving advice, I have not compaired these transmissions, and untill I got my '99 van 3 years ago, had never known anything about Fords... however, I'd like to help you get answers to your questions, and if such a swap is fesable. If I were close to you, I'd offer to help, as I have a spare trans for my van sitting in the garage in the event mine goes out.
Not knowing your location, that may be of little use to you. However, I would sugjest finding a spare of the same model and rebuilding it, as you would be able to swap one for the other without drive shaft mods, and every thing being direct bolt it stuff. Perhaps you like the C6 because you already have one and might be more comforable working on/rebuilding it... I can understand this.
I also could get you a phone number for the guy who rebuilt my trans in my truck, maybe just talking to him might help you find the answers you seek. If you'd like it, PM me and I'll get it to you. He was of great help to me, good work for a very reasonable price. Complete rebuild for $1400, including remove and reinstall the trans. I've put 30K miles on it.
Hope you find some answers that satisfy you...