We don’t know where the nails went. Science supports that the hands alone would not be able to support the body of Jesus, but the Romans could have used ropes around his arms to support his weight.
As for the stigmata…why do the wounds have to be exactly like those of Christ? In those saints who received the stigmata, there is a profound union between the saint and Christ crucified. For example, saint Francis of Assisi had a vision of Christ crucified, and then he received the stigmata. Stigmatists seem to get it based on their conception of the crucifixion. There are other stigmatists who live in our century who have received the stigmata on their wrists. There is a psychological element to this that cannot be discounted, but why can’t God work through our psychology?
The same thing goes for visions of Mary or Jesus. You can find several descriptions of Mary that are often very different. For example, compare the Mary of Guadeloupe with the Mary of Lourdes. There are differences. The Mary of Guadeloupe is…well…more Mexican. The Mary of Lourdes is much more caucasian. The Mary of Fatima also had different features. But this does not invalidate these miracles and visions. For me, it shows that God is working through our human psychology.
The Jesus I have a personal relationship with is a Jesus unique to me because my relationship with him is unique to me. The Jesus I envision probably looks very different from the actual Jesus of history. And he also speaks English. He knows everything about my life and my world. He know about my wife, my two kids, my job, my house, my car etc… because he knows me.
If Jesus appeared to me today, as he was two thousand years ago, I would probably not recognize him. I believe that if he did appear to me today, he would probably suit his appearance to fit my psychological and societal framework. Our God created our minds, and he can use our minds to communicate with us.