Upper Room: Friday began at sundown on (our) Thursday. They met in the upper room. While I doubt very seriously this is the room, this is the site you visit on tour:
Garden of Gethsemane: This is the garden. They've found a cave near here that the disciple's might have hid in when they weren't praying.
Jesus taken to the high priest: Very likely up this path.
Prison where Jesus may have waited to see Caiaphas the high priest:
In the wee hours of the morning, Jesus talks to the high priest. Peter denies him three times. He goes before Pilate.
About the third hour, nine in the morning, he is crucified at Golgotha, the place of a skull. This was likely in a quarry just outside the city wall. The wall has moved so it is currently within the city walls, likely in the spot occupied by the Church of the Holy Sepulchre.
The skeleton of a crucified man named Johanan has been found. His body indicates that nails weren't placed in the palms but higher up the arm, perhaps even between the radius and ulna bones. The knees were apparently buckled and a nail put through the ankle bones.
The Discovery Channel's "Jesus: the Complete Story" has a very plausible version of what it might very well have looked like. It will be on practically every hour on Saturday. Here's the best rendition of Johanan I have found on the web (Jesus would not have had a loincloth):
Here is the traditional, and I think as likely as any, spot of the crucifixion:
About the ninth hour, 3 in the afternoon, Jesus gave up the ghost. There were some tombs near the quarry. His actual tomb may have stood in this spot (although between Christians removing rock to isolate the tomb and medieval Muslims destroying what was left, well, there's nothing of the original rock remaining.
But here's something like what it might have looked like originally: