I had the exact same issue on my 4Runner ('99 Limited A/T). After a lot (A LOT) of troubleshooting and reading online, I narrowed it down to the Instrument Panel Circuit Board (Part 83861-3D260). It's the blue "sheet" that sits behind the gauges (2:40 in the video). Turns out after twenty years and 300k miles, some contacts wore loose or something, I don't know. Anyway, I replaced that and voila, it solved all those problems! Here's a video from Timmy the Toolman that should help you remove the guages. And another VERY helpful link from smallfry from the T4R forum. Good luck!
YouTube
Transmission Issue????
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