If yoke is hitting the flange its connected to (via the ball joint), then you should be able to see the two come in contact with each other when the driveshaft is on the vehicle. If the two parts do come in contact with each other, they should touch at around the "6 O-clock" position on the flange. Of course you just have to put the vehicle in neutral and push it slightly forward or backward until the yoke is vertical - at which point one of the yoke's ends should be at 6 O-clock and the other at 12 O-clock. But do let us know whether or not its hitting after you spray it with some paint.
Originally, when you said that your transfer case's front output shaft is facing up a bit, I thought that maybe the shaft bearing support was really loose. But it looks alright from the images. If you have the driveshaft disconnected from the transfer case, I guess you could shake the output shaft horizontally and vertically to see if there's any play.
If you have an angle finder and you have the driveshaft out, it might be worthwhile checking the angles of the front differential's input and the transfer case's front ouput.
