2003 Shifter Vibration 5th gear Manual Transmission

I took out the automatic transmission from my 2004 PreRunner and installed a 2003 R150F transmission (w/ transfer case and proper parts needed). During 5th gear my shifter starts to shake (has different degrees of shaking). If I get out of 5th and back into 5th the problem sometimes goes away (shifter feels smooth). When the shifter is vibrating on 5th, I downshift to 4th and go faster than I was on 5th and get no vibration. Shifter vibrates only on 5th gear no matter speed or RPM. I have replaced the center/carrier bearing and nothing. I kept the x-member from my prerunner because I read that can be used for 4X4. I have the correct transmission mount on the R150F. I replaced the mount that it came with because I noticed it was dented. I have no front driveshaft at the moment. I am just using RWD. Three "tranny experts" have said nothing wrong with transmission, it is something behind it. I have been at this for 3 weeks. I had them rebuild tranny and still vibration on 5th. Nothing has been done to the transfer case. I am waiting on the x-member that came with the R150F tranny to see if there is a difference. I also noticed that the carrier/center bearing cannot move to get the drive shafts lined up "by eye". My dad and brother have been helping and were are running out of options. I would like to compare with a 4wd manual J-style transfer shift, bit I don't know anyone with one in the San Antonio area. Any help would be greatly appreciated.