I take it when you say "top half" and "bottom half" you are relating to the picture and to the two piece drive shaft?
bottom half (short shaft)- mates to the tranny.
top half (long shaft)- mates to the rear end.
I must be missing something here, if I read both of of your posts (Staceman, 4Crawler) it sounds like the statements on which end of the the shaft needs rotating conflict with each other.
Is the part of the shaft with red line correct or the part at the top of the picture ?

It looks like to me you mean the top half in the picture which mates the rear end is out of phase and you would need to seperate the long shaft at the splined slip yoke rotate it 90 degress (1/4 revolution) and hope you are not out by 180 degrees, correct ?

If you rotated it 180 degrees you would end up woth the same orientation.

I found this write up on jeep applications on the subject of drive shaft phasing:
http://jeepgarage.free.fr/OWN/drive%20shaft%20alignment.pdf

It should still apply to my drive shaft combination, note "Dual Shaft with Slip Shaft" references in the diagrams.

Comparing the two piece drive in the picture to the Dual shaft with Slip shaft diagram in the pdf it looks like they have the same yoke orientations (phasing), am I wrong here ?