I have been using the rear end for 2000 miles prior to the t5 install and it's fine. Because I'm such a impatient guy I already removed the teams from the truck and took it apart. I think I found my issue. Just before I took it out of the truck I wiggled the output shaft at the end and it had lots of play. After the trans was out I tested the input shaft and it was moving in and out. All the time I took making sure I had no end play during the original rebuild was for nothing I guess. Wonder if things just seated and settled within the first mile thus causing this play.
Also the case bearings holding in the new countershaft were also allowing lots of end play now so it was moving forward and backward easily by hand.
Taking the box right now back to my
shop so I can press in the case bearing more to take out the end play
I wonder if that play in the input and output shaft was causing the vibration and the slightly annoying whine.