If rotating the driveshaft 180 deg doesn't stop the vibes, there are really two possible causes.
1st, the vibes may have damaged a u-joint. Once a cap is trashed, the shaft will vibrate. I think that you might have noticed any stiffness or noise when the driveshaft was pulled to allow you to tighten the output yoke nut.
The other possible cause is the loose nut may have allowed the splines in the yoke to wallow out. You may need a new output yoke. I had to replace mine due to a manufacturing error (the bolt holes were mis-drilled). Tom Woods has replacement yokes for about $75 plus shipping.
My symptoms were just like yours, all due to only 0.035 of an inch off center so it doesn't take much to cause significant vibrations. I had to use a old ball yoke (the part of the driveshaft that bolts to the transfer case yoke,) and a dial micrometer to discover the problem on mine. Once I swapped out for a new output yoke, no vibes!
Hope this helps..