Step 1 lock the hubs in, leave it in 2 wheel drive and take it for a run. If it still vibrates the it is from the transfer output shaft through to the wheels. If it does not vibrate then it is probably in the transfer case.
Step 2 remove the front shaft and lock the hubs in. If it still vibrates then it is in axle. If it does not vibrate then it is in the shaft or the alignment between the transfer case output and the axle pinion input. (index axle and/or double cardan driveshaft)
Also check the splines on the slipshaft of your front driveshaft . A common problem I have found (with land cruisers fleets in Australian) is that the front shaft sits in the same place for a long time (only turns when in 4x4). This lets the splines vibrate and wear in a single plane. The real fix for this (after replacing the splines/shaft) is to make sure that you either lock the hubs in once a month for a few miles or put it in 4x4 with the hubs unlocked for a bit of a run.
Now the other question is where are you running at over 40 in 4x4?
. Do you do it often enough for it to be a problem that needs fixing?
My E350 diesel with an Advanced Four Wheel Drive conversion has the same problem. I am not too concerned as the I do not do much high speed 4x4 driving or drive with the hubs locked (except in the snow and ice which is not too much of a problem in Phoenix) and then it is a good reminder to slow down.