When a SOA (spring over axle) is done there are a multitude of things that can cause vibration.
One of the main causes is drive shaft angle.
When I did mine, I had to have the rear drive shaft lengthened by about 4" and the front one by about 3".
If you are going to have it done have them install a CV joint, it will make a world of difference.
The stuck in 4WD could be an issue with the transfer case, maybe there is a vacuum line not hooked up, or the vacuum switches on the firewall.
Can you put the transfer case shifter into neutral and does the light on the shifter (the one below the AT Temp light) come on?
Here is another place to post up your questions.
http://forum.ih8mud.com/60-series-wagons/
The Mud board is kind of the definitive place for Cruisers!
Good luck!