To maximize the effect on the subject, it's better to strip him before he starts experiencing serious physical discomfort. Otherwise, pain and shame are competing for his attention. We want him to by fully aware of the humiliation of being stripped naked while the onlookers whistle and shout ribald taunts at him.
If flagellation is part of the program, then the stripping should precede it. I'd personally omit the flogging, since I think that scabs and weals and cuts detract from the appearance of a strong young body struggling in torment. I can't seem to get aroused by the spectacle of Jim Calviezel as 150 pounds of naked hamburger. However, as the Romanophiles in the group might point out, de gustibus non est disputandum.
In a crucifixion involving nails, the subject should definitely be stripped naked before being nailed to the cross. Once the cross is upright and his full weight is on the nails, he's going to have little attention to spare for anything else.
Even when tying the subject to the cross, I think it'd be better to strip him first. My own limited experience and the accounts of others indicate that physical suffering begins as soon as one's weight is carried by the ropes. We want the subject to be concentrating on that, and on his futile efforts to find some position that'll ease the torment. If we strip him at that point, the pain will keep him from fully experiencing the shame as his remaining clothes are torn or cut away, and the stripping could actually provide him with a brief distraction from his physical discomfort.
