You may have some worn out motor or tranny mounts, allowing the drivetrain to move around to much under high torque conditions (like when using 4-LO). Might check the mounts (a jack under the oil pan works well) and maybe add a chain around both motor mounts to limit the movement:
- http://www.4crawler.com/4x4/CheapTricks/MotorMount.shtml

See if you can determine what sort of motion is pushing the linkage out of gear.

I have also had few folks who had to modify the A/T brackets a little to work with their particular setups. In most cases they had to cut the main bracket down in height, so that even though they had say a 3" lift, they cut the bracket down to a height more suitable for a 2" lift.

I had a similar problem on my '85 (manual) with 1" body lift. In 4-LO going downhill there was enough body-frame flexing to pop the t-case out of 4-LO.

A drivetrain lift would be another option to minimize the effects of the body lift.