Noisy Rear Gears, or What

Just swapped out the 7 1/4" rear end in my 65 Barracuda last week because it was making noise. Found a used rearend that had been sitting a long time and swapped it in to have the same noise. I cleaned out the new(old) rearend (had some rust on the ring gear but mostly it was just cruddy inside) and used new gear lube. I used the axles that come with the rear too.
The noise is not as bad as before but still there. I know this was a low mileage rearend and except for have been stored outside for a long time I assumed it was good.
I cannot believe I have 2 bad rear ends, so now I need to figure out what else the noise can be coming from. Not the transmission the sound is from the back of the car, what about the driveshaft? If the u joints are crapped out would they be noisy or just start to clunk and shake?
Any other ideas?
Will it quiet down after being run awhile if it there was rust on the gear set or bearings?