definitely before. some shoes come ready-made with the holes in, but most farriers i've known prefer to punch the holes through themselves when they've shaped the shoe to the foot, and it's still red-hot. they punch through from both sides (quite an art to get the 2 to meet up perfectly i reckon) and then make the threads. this has to be done from the correct side, otherwise the studs fall out (as i discoved to my cost at 1 event after my last farrier did 8 holes from the wrong side..!)
Put some rubber stud plugs in the holes before you turn out, or if you can't get them, packed cotton wool and vaseline or similar. Otherwise you'll probably find a stubborn bit of grit in the hole that won't come out when you come to put the studs in. Another tip - put a pair of tweezers in your stud box, essential item but they don't seem to come with them.
Farrier does them before he puts shoes on but does them while he is at the yard, as in if i ask for them when he arrives i get them so hopefully yours will be the same.
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and then make the threads. this has to be done from the correct side, otherwise the studs fall out (as i discoved to my cost at 1 event after my last farrier did 8 holes from the wrong side..!)
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Not entirely true, the stud hole can be tapped from either side of the shoe and it will work just as well.
The holes are punched, usually to the size of 3/8, after the shoe is forged into shape and at the cherry red heat, Two hits on on the surface side and one on on the fullered side.
After this the shoe is cooled and the the hole is tapped, the tapping allows for the studs to be screwed in. If the stud hole is too large it is useless and i think this is probably what you discovered.