When a similar thing happened to my 4Runner, it turned out to be the flex PCB on the back of the gauge cluster... that may not be your issue since you seem to be able to 'change' what's going on when you mess with the tail light area of the wiring, but it is something to think about.
Besides the tail light area, that is the only other place where the wiring interacts between those systems. Do your shift indicator lights on the cluster also light up oddly with the turn signal ('99+ auto cluster)?
-Charlie
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'99 4Runner SR5 Auto -
4WD swapped
'89 Camry Alltrac LE 3S-GTE 5spd
'17 Chevy Volt Premier
'16 Honda Odyssey Elite
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