I would also verify your universals are all greased up and are without ply. As they can get noisey when one is going to fail. Mostly they produce vibration as well before failure.
Nothing wrong with exchanging your fluid cleaning the magnets and changing your filter. Automatic transmission love clean lubercating fluid and a clean filter as the fluid can flow properly..
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7 3rd gens listed in the build thread (2 are parts mobiles)
Build Thread:
https://www.toyota-4runner.org/3rd-g...os-builds.html
Brillo's Bucket Fluid Ex changer:
https://www.toyota-4runner.org/3rd-g...ml#post3358086
Sparks Plugs Wire and Coil Information:
https://www.toyota-4runner.org/3rd-g...on-5vz-fe.html