Conencted to the center ujoint is a 8" splined rod that inserts through the front part of the driveshaft and center bearing. While removing all the ujoints from the driveshaft for replacement, I am not sure if I marked the orientation of it correctly. I still ahve the orientation correct for the main parts of the driveshaft. Will this make a difference with vibration?

The driveshaft may have index marks on it already. Look for the small arrows stamped on the shafts in front and behind the center support. On the picture in George's reply they would be right above the 'g' in bearing and right under the 'R' in rear shaft. If they're ther just point them at each other.
The two small diameter driveshafts that I have don't have the markings but the 50.8mm that's in my car does.
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'80 DL 2 dr

I am not sure if anyone even understands what I am talking about.

There is a yoke thing that flopps around on the end of the rear half of the driveshaft. When taking apart the driveshaft I marked the relation to the main rear shaft to the front shaft. What I didn't mark was the relation of the center yoke. While removing the Ujoint between the rear shaft and the yoke thing, I messed up its relation to the rest of the shaft. The main parts of the driveshaft are still aligned to one another, but the yoke isn't. Can the yoke itself if not flipped the right way when I install the Ujoints again cause vibration issues? I didn't flip the ENTIRE rear half, just might have marked the yoke 180 degrees off in comparison to the rear half.

As far as I know the yoke with the splined shaft could be off 180 from what it was and you'd be okay. It's the shafts themselves that are critical. Just make sure the yokes are in phase like George suggested. Maybe that's what he was saying and I misunderstood him as well as you.
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'80 DL 2 dr

http://www.uwm.edu/~keobrien/car/driveshaft/IMG_0924.JPG

http://www.uwm.edu/~keobrien/car/driveshaft/IMG_0925.JPG

Those are pictures just to make sure we are talking about the same thing. One shows the yoke flipped one way.. one shows it flipped the other way. The driveshaft section doesn't change position, just the yoke.

Yes. That's what I finally figured you were saying in my previous reply. Just line them up like in the pic.
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'80 DL 2 dr

That center splined rod and the socket it goes into is called a "slip joint"
and it allows for minor length changes. If not assembled correctly it also
allows changes in rotational velocity in a sinusoidal pattern twice per
rotation. The yokes on each section of shaft (the one WITH the slip joint
and the one WITHOUT the slip joint) need to be aligned with each other so
you can look at the section that is together and see how the one that is
apart needs to go together. Put the tranny in neutral so you can turn it.
The pic below shows a properly assembled shaft:



If you put it back together like that it will be OK. 180° errors are OK,
any others will screw you up and give you pulsation in varying amounts,
worst being at 90° off where the variations in rotational velocity are
doubled rather than canceled out.
--
George Downs, Bartlesville, Oklahoma, Central US

George, I once installed the rear part of the driveshaft in my '84 180 degrees off and there was a problem with vibration at low speed. It's best to put it in exactly as it came out.
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'80 DL 2 dr