I too had all these concerns after seeing the Passion, when it was first released.
The historical issues became a problem, until I thought about it further.
Keep in mind, I’m not saying this is the way the story went absolutely, but just an explanation for how Katherine Anne Emrich saw it.
First, the full cross. Historically, you are correct, the condemned person would most likely carry just a cross beam as the two thieves in the movie did. However, according to Emrich’s dream, the high-priest Caiaphas, was concerned about anything going wrong in Jesus crucifixion and death. So, he had the full cross erected for Jesus. He had planned to have Jesus crucified, well before his arrest.
2nd, the nailing of Jesus to the cross. at first I had a problem with the predrilled holes in the crossbeam. The Romans would not have done this.
However, Caiaphas most likely heard the prediction of Jesus rising from the dead. Also, there were times in Roman crucifixions, where bodies did fall off the cross. Caiaphas, wanting to ensure this didn’t happen to Jesus, which would’ve given a sign to the people that Jesus was the Messiah, he had the holes predrilled, so the nails could bend back on the backside, as they did in the movie.
As far as being nailed through the hands instead of the wrists, we have to keep in mind that when Katherine Anne Emrich had the dream, it was interpreted according to her own level of intellect. People had no idea about crucifixions until the past 50 years when we learned that most likely, the person was nailed through the wrists.
However, there is also the probability that the condemned first had their arms bound to the cross with rope, before the nails were driven through their hands and those ropes were kept in place until their deaths.
Japanese crucifixions match this scenario.
The bottom line is, Katherine Anne Emrich’s dream is mystical, not literal.
The contemplation received in reading the book and then seeing the movie, moved myself and my wife deeply.
Jim