It would be ideal if you reinstalled everything the way it came apart. Whenever I play with the driveshaft, I always match-mark the mating flanges at both ends. In theory, though, since the DS is balanced as a unit off the car, presumably any flange orientation at either end should be OK.
I have no doubt you have a DS vibration because of the speed range you mention. Is there a chance you're still off a spline tooth between the fore and aft DS halves? Also, make sure that the both yokes on the DS are parallel - that's mighty important.
When the DS was off the car, did you check the U-joints? That might be your problem.
The other thing that might enter into the fray is if you had your torque rods off and *somehow* upon reinstallation the rear axle is no longer square to the driveline. That would add a lateral misalignment to the driveshaft, which could create a problem with symptoms similar to a bad U-joint. If you think that's possible, I would just un-torque them but not remove them; load the trunk or cargo area with 100 pounds or so, and bounce the car a bit to get the rear suspension in a neutral position, then re-torque.
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Thank goodness we don't get all the government we pay for. -- Will Rogers
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