I have a 96 Tracker and when I lock the hubs and put her in 4 I get a real bad vibration on the passenger side.  It goes well for a couple of minutes then every time I give her gas I get that almost grinding vibration like gears aren't lining up. I took apart the hubs and they are working fine.  If anyone could help I would be much obliged. 

Well, it could be a bad CV joint.  Of course it is...the passenger side CV axle is the one that's hardest to change.

Check the back of your rotors for wear and wour wheel bearings for play. My 89 would get a drag onthe brakes when the bearings got worn and would make a grinding/drag noise while in 4x4. The noise was the rotor dragging.

Zig

Thanks I'll check the CV joint.  That would totally make sense because it makes noise when the hub is locked to.  But would it make the whole car shake.  I've had bad CVs and  they just made a clicking not a total car vibration. 

Check the T-case mounts, they might be bad and making the front drive shaft grind on the x-member

Wild