The two piece drive shaft should cancel out any phase angle issues created by the universal joints difference in radial velocity. If you are talking about balance that is another issue entirely.
Any time you disassemble anything that rotates; whether tires, wheels, drive shafts, even gears, and there is more than one possible way it can go back together then you MUST mark the rotating part before you take it apart so you know how to reassemble it again. There is a difference between a static balance and dynamic balance; and rotating parts have a way of illustrating this difference.
Vibrations in drive shafts are most often caused by angles refered to as the pinion angle. Because the drive shaft is rotating in a circle only when it is collinear (in a straight line) as soon as you induce a bend (make an angle in the drive shaft) the drive shaft acts as though it where rotating elliptically, gaining speed in some parts of the rotation and slowing down in others. This is called a change in the radial velocity. A drive shaft must have the angle exactly the same at each end of the shaft, only with a different sign (one end pointing up the other end pointing down), so that the two changes in speed exactly cancel each other out. If not you get a very annoying vibration that changes with vehicle speed. (If you find a major harmonic by speeding up or slowing down it can shake badly enough to break parts).
I would rebuild the tranny and use a six inch tail shaft. It will require you to find a shorter out put shaft and the shorter tail housing, but then the factory drive shaft will fit without issue.
The nine inch tail shaft was out of a truck or big car with a long single drive shaft. A rebuilt tranny offers piece of mind and allows you to add any heavy duty parts and a shift kit. Nothing worse than going to all of the bother of installing it only to pull it later because it is slipping or has other issues.
No idea! I never worked for GM's design team back in the early sixties 60's. I was still in college getting my engineering degree (then I took a short vacation from engineering as I learned to fly over beautiful southeast indo-china, aka Vietnam).
Shorten the front driveshaft. I did that with my '62 bel air changing from the PG to TH350. If you grind the weld off the yoke, there's a nipple on the inside of the yoke that slide into the driveshaft, so the driveshaft will always be centered with the yoke. Carefully cut off what you need with a chop saw, spot weld it back together, check length, then spot weld around the whole driveshaft until you welded the whole joint.