Interestingly, as far as BDSM crucifixions go I think almost everyone who has actually hung on a cross for any period of time has mentioned that the worst pain they experienced was in their shoulders. Some said it felt like their arms were being torn off. I think this is mainly due to fastening the wrists with the arms outstretched on the patibulum, which will greatly multiply the pull on the arms due to the victim's body weight, sometimes dangerously so.
As far as the worst pain that a real crucifixion victim would have experienced, we obviously can't say for sure without interviewing a real victim dying on the cross. My guess is that the worst pain they experienced was just before they died, since the trauma of the nails, sedile or cornu, sunburn, possibly abrasions to the back from rubbing against rough wood, only increased over time.
I would say that the greatest fear, horror and shock occurred when the nails were being driven in. That was when the last vestige of hope vanished and was replaced by panic and the feeling of absolute helplessness. The actual pain from the nails might not have been that great initially; typically with an injury like that, the pain follows after an initial shock. However that may have hurt, I think that the further shock when the patibulum, along with the victim, was lifted so that all of her weight was hanging against the nails in her wrists was an agony that likely caused many victims to faint.
So how did a crucifixion victim experience agony that could have actually increased over days? Did they get "used to" the pain? I think the key is that, as bad as it was, once the victim was nailed and hanging on the cross, most of the increase in pain was gradual rather than sudden. The exceptions would have been cramps and the sudden pain when they shifted their weight from wrists to feet and vice versa - something they probably learned had to be done gently and gradually.
Again, this is something we will likely never be able to say with any certainty.
Jedakk