Hi guys,
I think the problem with the rear lights and cruise control cancel, may come from changing the double wolfram lightbulbs that are originally installed in the brake lights, with LEDs that to do not correspond with the oem wiring harness. The oem bulbs, when you remove the from the sockets, you will observe that they have more contact surfaces, I think 3(when common ground is used) or 4. In the wiring loom, the wires that supply ground and voltage are 4, 2 for ground and 2 for voltage. The order of these 4 wires in the connector is specific the light bulbs structure. One set of ground and live wires is for the bulb's tail light wolfram wire, and the other set is for the bulb's stop light's wolfram wire.
When you switch the bulbs with LEDs, LEDs are voltage oriented, and some manufacturers have designed their LEDs with same contact design as that of the OEM wiring loom, but not all. In their installation instructions, they mention that, if after installing them, one of the stop light or tail lights circuits dont work, removed them and installe them in reverse in the connector. It may work, but not for all car manufacturers.
So the problem comes when you installed a set of LEDs with the wrong harness polarity and common ground. To fix the problem you have to remove the pins from the connectors in the wiring loom and reorder them in the correct order for the new LEDs. Otherwise, a common ground on the LEDs can complete a brake circuit and thus cause а cruise control to register that the brake pedal has been depressed, and cancel the set speed.
The OP's problem may be not be related. The brakes and cruise control circuits are connected. The blinkers and cruise control circuits are not.
The OPs problem may come from maybe a secondary alarm being connected to the blinkers and could be connected to the cruise control circuit to be fed 12v.
Depending on the year of the 4runner, there are two CC systems. One has separate CC controller and actuator, while the other is one box in the engine bay.
There is a diagnostic pin in the dlc too on some models.
Hope this helps a bit, although it is not a solutuion.