5th Gen 4Runner transfer case whine after 4.88 regearing

My lift was installed in 2016 and never caused any noise so I don't think it's the pinion angle since that hasn't changed at all with the re-gear.

So the pinion angle would have changed a little with your lift, but on stock differentials it probably didn't matter. After installing not only new gears, but a new gear ratio; there is the possibility that the difference in loading/transfer of torque (which is why we re-gear, to adjust how torque from the drivetrain is delivered through to the wheels) could maybe cause something in the transfer case. Like most US
us have said, it's something to consider as a contributing cause, but unlikely.

Something you can try is to remove the rear axle shaft, then operate the vehicle in drive and see if the noise is still present (keep in mind the vehicle will be basically in neutral like this when you're in 2WD, so don't be super aggressive on the throttle.) Then put the vehicle into 4HI (basically turning the 4Runner into FWD at this point) and drive it a short distance to see if the noise goes away/is present still, I don't recommend driving it at freeway speeds in this configuration; but a short distance at 30mph on relatively flat/ even pavement shouldn't cause any significant damage (we will do this FWD "mod" sometimes on vehicles that have blown their rear end or have had rear end damage to limp them in and out of the shop, also done it on the trail for one or two guys to get them back to base camp).

It's a bit easier to do with the vehicle on a lift or even 4 jack stands with all 4 tires off the ground, but I don't know what your work space looks like, so I'm trying to giving options for the "lay person."

Post note- you mentioned it sounded worse at the rear output shaft flange of the transfercase? Have you inspected/tried greasing the U-Joints and slip yolk and seeing if that changes anything? U-Joints don't usually make a whining noise from what I remember, but then again most of the ones I've seen are obviously failed and knocking, so maybe one starting to fail could sound whiny?
 
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