Hello!
First off, hope the training is going well.  Sounds fantastic.  Secondly, a bit about myself:  I've been running barefooted for just over a year now and have recently done my first marathon, doing it barefoot, naturally.  Now, to try and answer your questions:

In my opinion, wait until after the ultra before making any fundamental changes to your running.  There's every chance that your gait will be different between running shod and unshod.  In my own experience, my running gait changes when I run with even so-called minimalist trainers on (which led coincidently to a rotten injury),  so I only run barefoot now.  I used to get knee and shin problems, which is in part why I started trying barefoot.  I started slow and alternated between starting a run in my trainers (Asics Cumulus's) and ending barefoot.  However, it wasn't long before I ditched the trainers altogether as it didn't feel right with the trainers.  When I was researching about BF running, many said that it was better to ditch the trainers and concentrate on cutting back and building up again with the new running style that BF running gives you.  
Other general points:  The skin on your feet isn't too much of an issue. With BF, you're not pushing off but lifting your feet so there are no shear forces that would cause blisters on your feet.  Give your skin enough time to recover - I normally had a day off after every run to give the skin a break.  Once things are established, you can run daily or as your plan dictates.  Important points are bones and ligaments.  Bones will take time to thicken and strengthen though with the mileage you're used to, that shouldn't be so much of an issue - the bones in your feet will need time to adapt though.  As for ligaments, barefooted, there isn't that cushion of padding between your heal and the floor so the achillies and calf muscles will be stretched to make up that extra distance, even before you start running.  Many have written that it takes up to 7 months for the ligaments in the legs to adapt.  It's not surprising to learn that achillies and stress fractures pop up time and again as injuries cited by people transitioning to BF running.
Look on the web and you'll find people who have ran ultras barefoot so it's entirely reasonable to go for it, though I've no idea how long it took them to get to that point.  A great source of info. is barefoot ken bob's website.  Jason Robillard is an ultra barefoot runner and another great person to look up on his website as your cause and his are the same!

Anyway, I hope I've been of some help, i'm by no means an expert.  Feel free to message me if you want follow up on anything.

Good luck!