I pulled the fuse for the transfer case in out 2000 when we got it in 2011. Been fine ever since. I did just use 4wd a month or two ago after putting fuse in to pull a large stump/tree around. It worked fine.
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My sister has a 04 Explorer Sports Trac and basically the same thing was happening. went thru tires, u-joints, differentials, transmission and it was still there. Finally took it to the dealer and it ended up being the transfer case engage motor. it still worked but was going bad and was the cause of the problem. I am not saying that this is your problem but I would think it's worth looking into.
The transfer case motor seems to be the go to item on the first and early second gen models. I have a 2000, that I run without the fuse connected, and have no issues. Unfortunately you can't just pull the front CV shafts and run it up the block. Your shop if their worth their salt, should be able to sort out your vibes.
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100%If the tranny shop didn't mark and reinstall shafts in same spot, a vibration will be felt. Happened to me years back on my 82 mustang 5.0. replaced front and rear u joints, but didn't mark the front, where it separates from the yoke. What happened was I got a nasty vibration above 50 mph. Drove that way for about 2 weeks, pulled the shaft, popped out front u joint, rotated it 180 degrees, vibration totally went away. Driveshafts are like tires, they need to be balanced. My guess is whoever owned your SUV, messed with one of the shafts. Well that's what happened to me at least.
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