How to trouble shoot limp mode?

Limp mode is usually the ECU reacting to a fault, so I’d start with finding the code instead of throwing parts at it.

First, plug in an OBD-II scanner and see what codes are stored. Then check the basics: battery voltage, fluid levels, loose/damaged connectors, vacuum leaks, and wiring around the sensors.

If the codes point to the transmission, start there. If they point to something like the throttle position, MAF, or engine sensors, test that circuit before replacing anything.

Also, what engine and transmission does your 4Runner have, and what symptoms are you getting besides limp mode? That would narrow it down quite a bit.