Dan, I hope I'm understanding correctly what you've done. I really haven't followed this thread, but I think I've caught up now.
Well, you got it to work, and that's good, but it's a two-edged sword. There's a reason that Unix- and Linuxen don't run as root unless it's needed, the main one being security (from others and from yourself).
Applications that now run from your root directory, with root permissions, shouldn't. *Folding at home* is an example of one. There isn't a reason for it to run as root, and its location should be in your /home/user directory. Running it as root, from your /root directory, could very possibly leave your box open to exploits (since the app calls home from there, and that's not a Good Thing.)
I'm sure that there are other examples as well. Kicking its ass, although satisfying from the perspective of finding a work-around for your mounting problem, will most likely create problems down the line, since you are now doing *everything* as root (since you are actually *logging in* as root.) Basically, what it means is, every file that you download to your machine, or create on your machine, will be owned by root, and that is not, in any way, a good scenario.
I'm pretty sure others here will agree that it isn't, so be very, very careful with file manipulations, because when you are root, (as you know) you can delete/move/rename/run/bork/lose/rub_into_your_belly/etc/etc *anything* (without confirmation as well) and the wrong move will plotz your whole installation, or maybe make it unbootable.
In the 5 years or so I've been running Linux, I don't think I've *logged in* as root more than a half-dozen times, and after I did [ONLY] what I had to, I logged out and went in as a normal user. OTOH, I use su - most every day to perform certain tasks, but I'm not logged in as root.
There really has to be a better solution for the automount issue. I don't know why the distro isn't automounting, but there are a number of small automount daemons that you might try. In my Gentoo boxes I use one called udiskie. You might see if it's in your package manager and try it.