I've looked everywhere for a problem similar to this but have not been able to really find something similar.

I took my 4Runner to an independent Toyota mechanic to to the valve cover gaskets and timing belt recently. Drove home just fine. No more dripping and burning oil smell and all seemed well.
The next night I decided to go for a drive and the idle was acting really weird when the engine was cold. It would start out fine, but then as soon as the idle started to slow down it would start surging like in the video. It only did this when the truck was cold. After driving a it a bit, I could start it again (still warm) and it wouldn't do this. The one thing I have yet to fully verify is that it it seems to only do this when the clutch is depressed. If I roll it back out of the garage without leaving the clutch in I couldn't make it do this. Also, another thing I noticed, is that depressing and releasing the clutch seemed to change the idle just a tiny bit. Not sure if that's related.
It also doesn't ever really settle back down to a normal idle. During the initial drive it hovers around 1000-1100 RPM at idle. If I shut it down and start it up again, still warm, It idles much rougher and lower. The other day it kept wanting to stall at idle but it hasn't really done that since. Just a low, rough idle when warm.

I sent this video to him and he seemed pretty confident that it's a vacuum leak. I would take it back to him but logistically it's really difficult as he doesn't live close by. I took a propane torch and didn't notice any change in idle. Also, the hoses I can see look good. I have replaced a number of them, but I'm just looking for input before tearing into stuff.
I have the FSM and it has a checklist to check. I also don't mind doing all the steps just to get familiar with my truck.

Thanks!

 

Definitely sounds airflow-related, possibly just a small tear in a vacuum line or improper routing, I had this exact issue when I had to daily mine, I just wish I could remember what exactly fixed it.

 

If yours is still equipped with EGR system i would check it for leaks, The EGR and Modulator diaphragm are prone to leaking when they start to get up in age. I just went through the same issue. I cant see spending the amount they want for the OEM parts so i will be deleting EGR, modulator, and Pair valve.

 

I guess I can double check the routing of all the hoses and replace them at the same time. I have the silicone vacuum line and I've don't most of them but not all. I also noticed the throttle body had a little piece of gasket sticking out and looked really old. I wonder if he replaced the gasket when he put the throttle body back on the plenum? I want to pull it off and clean it anyway...
I just mainly wanted to know if that really did sound like it's related to airflow or something else. The guy who did the work seems to know Toyota really well so he's probably right.

 

I've seen a couple videos online where people go through the entire testing process to see if it's the EGR or something else...seems like a good exercise to go through. I don't want to get rid of the ERG/PAIR if they are still working but if they are defective then I agree...the OEM pricing is nuts and they will go away.