Heres a short explanation of what you should have.
The top shaft you DO NOT want. The U joints are put there for a reason. When the trans, shaft, pinion are in a straight line, the bearings in the U joints will not rotate and therefore will not lubricate themselves. Bearings will fail much faster.
The second shaft is what you want. Both trans and pinion are parallel to one another with the shaft at an angle. You can run any angle on the shaft as long as you don't exceed the U joint angle specs. As stated earlier, FORD allows .5 - 3.0 degree difference between the trans and pinion. So you don't have to have the both trans and pinion at 0 parallel.
I would suspect that yours looks similar to the 3rd shaft. And would require a shim to help bring it closer to parallel.
The last shaft is self explanatory. But if yours looks like that, then you need to get it corrected quickly.