As far as the original vibrations you posted about I got my Money on a bad D/S & or output shaft bushing....I quickly read through all the post and dont think i missed anything..
I would pull the D/S and check the yoke aswell as the output/tail shaft bushing. What prob has happened is since your D/S is bad the yoke has been unevenly riding on output shaft bushing and has finally gotten so bad it feels like the car is gonna fall apart. It doesnt hurt to crawl under the car for 15min and check things out and at worst u may spend $20 on a stock driveshaft and $5 on the output shaft bushing.

Also i have seen bad motor/tranny mounts cause the yoke to rub unevenly on the outputshaft bushing...Your D/S may be fine and depending how bad your motor/tranny mounts where before you replaced them you may of wore out your yoke and output shaft bushing to hell!

-Anthony-