I have had my T4R 5 speed for several years now. I started having issues with the cruise control. I would turn it on, have cruise light up on the dash, but the speed would not set. I take some long trips and use the CC several times a week. It turns out the clutch pedal was not returning all the way up. There are 2 sensors on the clutch and 1 on the brake. They are small white plastic push buttons. I had removed the large clutch spring when I got tired of replacing the plastic bushings that would crack and cause terrible squeaking. At True Value you can buy a #70 barrel spring that will help to hold the clutch pedal up in place. It cost about $3. If you need a stronger spring, buy the brake pedal return spring from a Toyota dealer. I found out about this in the Toyotech forum. My CC works fine now. Thank you fellow posters!

This is from the Toyotech forum:
There is an adjustment for the clutch pedal under the dash. If it is out of adjustment, the cruise control will not engage. Look under there and you will see a small white thing that the clutch pedal pushes on when the pedal is depressed.

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I have this same issue. Can you post a picture of the spring you added?

Wow, really good to know, worth a try. My whole assembly has been worn out for a year or so. Always pulling the pedal back to myself with my foot.

That's how mine is with 250,000 miles. How many miles on yours?

This is exacty the fix I did on mine wich I read about here from someone else's build thread. Except I used a brake pedal spring from an auto Tacoma in a junk yard. Cleared my cruise issues right up. Still occasionally catch myself bump the cutch pedal up with my foot out of habit though.

Apparently the Tacoma's use a linear pull spring for the clutch but Toyota went with a "barrel" spring for the Runner as when the spring is all the way down it actually helps hold the clutch pedal down. Supposed to be for more "luxury" or whatever. I notice not difference with the constantly increasing resistance linear pull vs the "barrel" except for my cruise works.

I added another photo to my original post. I hope this helps.

My rig is at just under 160,000 so not close to yours, surprised mine has gotten worn out so fast. Thanks for adding the pic!