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Welcome, I'm Chris (aka Moose) I prefer to work when others don't, I am here around lunch and after dinner till after midnight.
If you directly apply power and ground to the shift motor, yes the motor should turn and change through the gears, however it will not know where to stop when doing this so I would not attempt to drive it this way because it will be partially engaged in gear (4 high-4 low). Are you needing the 4x diag steps?
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The noise comes from within the transfer case, not from within the motor. Are you remote powering and grounding the motor with it on or off?
The clunk will only occur if the is alot or a slight amount of stress or bind inside the transfer case. If all the gears are lined up, it can shift from 2 to high to low without making much to any sound.
Hello again Chris here,