I picked up a W250 a while a go and it seems everything but the Cummins was only built to go about 80k miles which was a long time ago. I just had the rear driveline rebuilt by Power Drive here in Wichita which every mechanic in town says is the best place to go.

When I take it up to about 60-65 (guessing because the speedo doesn't work) it begins to vibrate and there is a whine or high pitch humming coming from the tranny. it gets worse with more speed.

My immediate thought was that they didn't balance the driveline correctly but the previous sloppy driveline might have been covering up this vibration. 4th gear wight he throttle mashed is fine so I am totally confused.

 

Bearings or rough teeth is my guess. 4th, being direct, doesn't load the countershaft... so there's a clue.

My worst Getrag growls in 4th and 5th (pops out of those gears too) and 2nd grinds on any attempted downshift. I still drive it though.

 

While installing the driveline I noticed the rear yoke on the transfer case was sloppy. I changed out the bearing and seal. The vibration is still there which kind of confirms my suspicion that its in the tranny.
Should i just rebuild the tranny or can i get away with a couple bearings?

 

Check your 5th gear there should be a nut that holds the gear on and over time they do back off unless you pin the gear or weld it in place

 

You really need to get it out of the truck and do at least a partial tear down (top cover, ext housing) for a thorough inspection and go from there. At this point you don't even know the condition of the major components.

Hearing, guessing, and ordering parts never worked for me... I don't do it anymore.