Maybe take a look at the engine mounts while the engine is out? It's also a lot easier to do the valve cover gasket job and timing belt job if you plan on putting it on an engine stand (if it's not already freshly done). Other than that, I cant't think of anything other than simple maintenance and maybe cleaning up the engine and engine bay. Maybe time to add some nice headers
Here's the part # for the RMS - 90311A0027
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'99 Toyota 4Runner LTD - Dual Locked | Geared | Mid-Travel | 35s | Armored