yotahuntr

Hi guys need some advice before I start throwing wrenches.
I've got a 94 toyota pickup that has a vibration that seems to be only in 5th gear, during acceleration and cruising speed, does not seem to vibrate in gears 1 thru 4 or if it does it is not very noticable. Long story short, I picked this truck up dirt cheap due to low compression in #4 cyl. I dropped a new motor from an 89 4 runner in it and it is running good and strong except for the vibration which has been there from day one and is driving me crazy. I've been on my back underneath checking for bad u-jounts and cv joints and such but everything seems tight except for the carrier bearing which has plenty of slop. It's a 2 part shaft and I see where the front portion has been replaced. My question is will the carrier bearing cause this? I also read where if the teeth in the front shaft are not alinged to the rear shaft it can cause this. If so how do you aling the shafts after the fact? Any advice would be appreciated, thanks.