Just make an order, and add in a comment box (in the ordering form) that your feet is X cm long and Y cm wide, and last time you had their shoes (Stem) it was Z size. Ask them to correct your order if an ordered pair is not good for you.
I would go the other way round - that is removing protection to its bare minimum, and I'd focus on your running form, because maybe with the longer weekly runs you're simply too tired to run properly, that is with good and healthy form (since your goal is now training for a 100mi, and not training for a correct running).
You can also make a running experiment & run for a week(s) on forest trails and other(s) on urban paths (asphalt) and check if that matters at all. If it doesn't, then it is your "bad" form that needs to be improved while training for a 100mi.
15km barefoot on a forest trail (1h34min) & it was awesome. This is not only my barefoot PR but also the longest run I've ever done (my previous PR was 12km on a road, in regular sport shoes & I remember that it was soooo boring).
Avoid TMTS and you should be fine at a 5k finish line (in 90 days) :-)
Just listen to your body: any pain should be a 1st warning that you're pushing to hard or doing something wrong (bad form).
It is up to you, but running barefoot at this transition stage should help you in not getting injured (your feet, blisters wont let you :-D).
Barefoot Ken book is an awesome lecture for a beginner (like I'm), so if you like to read, get a copy and read it - it is very well written.
As for a couch plan... just run, but not too much too soon (TMTS) and enjoy! (find the most gravel road in your area that you can think of (impossible to run on for a "normal" person), and start there, this - as well as being barefoot - will help you in your training) :-D
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+ 8km of cycling back home (in minimal sandals) 
