If the discomfort stops when your muscles are warm, then just warm them up before running (the little walk is not quite enough).
Just stand up and lift (so you are on your toes) and lower your heels repetitively for a few minutes quite fast, some lifts straight up, others with some rotation to warm up the ankle and feet muscles as well as the calf. The calf should start burning by the time you are warm enough. And when it does burn, take a small break and do it again a little longer. If I didn't do this, something would hurt somewhere in my lower leg each time I go running. In your case it's the heel, so make sure that when it has to work it does not do so while cold and stiff, it will only add to the small injury it already sustained and that created the disconfort. I hope it makes sense.
In regards to the toes touching the ends of the pockets, that is only crucial on the big toe or your longest toe if you happen to have Morton's toe. My big toe gently kisses the end of the toe pocket on almost all of my VFF and my other toes are not even close.
In your case Mr Leigh, from the picture on your sizing thread, you have tiny toes, I'm surprised they touch any pocket at all . And I can't help you with the KSO's or Komodos, ScottishBFR, since I don't own them. Bad enough the Bikila ended up being the wrong size anyway... I am not worried about your big toe in the 38.
No, unfortunately they look big, most of the toes should touch the end of the pocket, and there should not be room behind your heel. So now you know that for VFF's your base size will be 38, it's hard to be sure until you really try them on.
24.5 inches, Morton's, neither wide nor narrow. 39 or 40 in Classics, 39 in Sprints, 39 in Treksports and Bikilas, 40 in Bikilas LS, 40 in Flows (39 is good in length but toes are squeezed), 39 in VB Boxing Boot and Lucy Lites, 40 in Off Road Hi and Evo II, 39 in Stem (now Lems).
My experience with calf pain is one of 2 things: too much too soon, or wrong form. By wrong form I mean specifically either leaning forward when running or landing too much on the forefoot (i.e. not using letting the heel touch down enough), therefore making the calf work too hard. I would be extremely surprised if "lack" of cushioning had anything to do with it.
Wow cool story! You followed your dreams. I can't help but see a similarity with Charlotte Brontë's "Villette" and "The Professor". In my case, my dream would be to live in Scotland or England one day... I am a Canadian who is a British at heart...
Yeah just saw that a minute ago, thanks. Good choice, the Magenta/Orange look great, I regret getting the Silver/Verde, I should have gotten the Magenta. But, as they will need replacement eventually, the purple Bikila LS are next in line.
Three way tie for me, I really can't choose: Slate/Palm/Lichen in Sprints, Sand/Dusty Blue/White and Yellow/Grey/White in Classics... However, since the white sole becomes stained so quickly, I could say the Slate/Palm/Lichen should win.
I just moved and I dedicated half of one of my new closets in the guest room (10 feet from the exit door of the appartment) to my VFF's. They are all neatly arranged by style and function in sliding metal baskets in the upper portion of that closet, the bottom shelves are for linens.
BFR, if you are comparing to the KSO, Bikilas are a bit tighter because of their thicker fabric. But each shoe is different and each foot wearing it too. For example I wear 40 in VB Evo II but 39 in VB Lucy Lite. I can wear Classics in both 39 and 40... And as Mr Leigh says definately don't compare to other brands. You will have to take a little leap of faith I am afraid...
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. And I can't help you with the KSO's or Komodos, ScottishBFR, since I don't own them. Bad enough the Bikila ended up being the wrong size anyway... 
I am not worried about your big toe in the 38.
