Driveline vibration out of now where! Help!

Update: Today i pulled the driveshaft only to find the u-joints are absolutely fine! Still just as smooth as the day i had them put in, no binding at all. I was hoping thats all it would be but no such luck. So i spun the pinion on the rear end and in turn, it spun the wheels, both forward (suregrip) and no noise. I had my grandson spin the wheels while i laid under the car where the rear end is and no unusual noise. So, i put the driveshaft back in, installed it 180 degrees off from where it was just to see if that would help. After i got the shaft bolted back in, i had my grandson spin the rear wheels again while i laid under the driveshaft and i could here a boom...boom..boom...boom coming from the tailshaft of the trans. So i scooted myself up under the tailshaft and had him keep spinning the wheels and sure enough, its coming from the tailshaft and i could slightly feel it in the tailshaft..So, im assuming this is where the problem is. Obviously he couldnt spin the wheels very fast but enough to make the pulsating boom and i guess when its spinning fast, it causes the bad vibration. I fired it up on the jackstands again and it seems to have kind of a slight vibration going all the time, but the pulsating bad vibration comes in about 40-45 MPH and way worse in 3rd gear than second..I can run it up to 45 in 2nd and its not near as bad as when it shifts into 3rd and at that same speed. I dont know much about transmissions so this really has me upset! when i bought this transmission, it was freshly rebuilt and when i got it, my friend tore into it to verify and it had been for sure. I bet i have not put 1000 miles on it since then, which has been around 2002 or so. It shifts fine and all, no slippage or anything. The ONLY thing i saw questionable when i pulled the driveshaft out was the shiny area on the front of the driveshaft that slides into the the transmission had some pitting going on and IF the tailshaft bearings used that shiny part of the driveshaft that slides into the trans as the inner race, then it would make sense as to this vibration being from the pitting..but i dont think its made like that..?