It looks to me like someone has adjusted the throttle stop position. This stops the butterfly from closing fully. Most likely this is whats happened...You idle air controller that controls the amount of air bypassing the closed butterfly and entering the engine has got clogged with carbon which is very common. When this gets clogged your car will stall at idle as no air makes it passed through to the cylinders. Instead of cleaning that, they have adjusted the butterfly stop screw (like ona  carby engine) so air is comming through to the cylinders but it keeps your TPS out of its idle fuel mapping position and also means your idle air control has no control on idle speeds. As they did this when your engines warm it probably idles fine when warm but has trouble when heating up. There are a few things you need to do to test this but its a bit hard to explain. I could be wrong but idle issues like this are usually related to your idle air controller and throttle stop position as these are the main things controlling idle speed. Over or underfuelling wont cause jumps in your idle speed that drastic.
It doesn't seem to be too big of an issue at all more of an annoyance. I'd leave it alone until things get worse if they do.

Ohh should also say vacume leeks are another common problem that could cause irratic idle.....probably the first thing to check.

track_mr2
Ohh should also say vacume leeks are another common problem that could cause irratic idle.....probably the first thing to check.

Now that you mention it, I had a boost gauge that I had to remove for RWC, and while the line going to the (now absent) gauge was plugged, this is when I had the engine stalling on cold start. Now that I have re-installed the boost gauge (and the throttle body got cleaned), I no longer get stalling, but rough idle on cold starts instead. So either the throttle body cleaning helped or this is related to the line going to the boost gauge (both things happened on the same day as well as re-installing the manual boost controller so it's hard to pin-point the reason for that change)
 
Checking for vacuum leaks seems like a good idea regardless!
 
EDIT: the re-installing of the boost gauge was irrelevant. I still get stalling sometimes on cold start.

Any further word on this?  I have something similar on cold starts and I'm interested in your progress.

Sadly, no. Sometimes my car starts and stalls after 2seconds, and sometimes it's just a very rough idle around ~500-700RPMs and slowly and painfully makes its way to 1200-1500 RPMs until it warms up and idle fine.
I did try to look for leaks, but I couldn't find any (next time I see a mechanic I might ask him to try to do it the proper way with a vacuum pump). Also my vacuum gauge indicate a steady ~500 Hg mm (~21psi in/mm) which seems pretty good, so I am not sure a vacuum leak would be the cause.
So my next guess would be TPS/ IAC, as someone mentioned above (I do not have the skills to check these out myself though) or the AFM adjustment screw (looks like the anti-tamper bung has been removed, so someone must have touched this and I do not know if it's been set up correctly).
 
I will post again if/ when I figure this out, but any help would be more than greatly appreciated!

Hi Alex, just read this post, I would suggest it is related to something you have recently done.  I never once had an idle or cold start issue with it whilst I owned the car.
I'm not sure exactly what you have done, changed, installed but I would be looking there.  Just make sure the TPS hasn't been adjusted as I know a few mechanics often play / adjust them and then all problems with idle occur.
 
As for blocking of the boost vacuum line, that would not cause at all.  Have you or mechanic performed a coolant flush by any chance?
 
 

Hi Mike, it actually happened for the first time on my way from Adelaide to Canberra before anything was touched. Maybe something broke during the long trip, I am not sure.
No coolant flush was done, however one of the line was leaking water/ coolant a little bit. The clamp was tighten up and a bit more coolant added.

I'm interested as to why you'd mention a coolant flush?
 
A troubleshooting step I tried was to replace the water temp sensor on the logic that the computer was misreading the coolant temp and therefore not fueling/etc correctly.  While it helped with my pinging issue, it doesn't seem to have done anything re the cold start.
 
Could be something to consider Alex.  
 
You can at least test it with multimeter to BGB specs although the water temp sensor isn't that expensive ($50ish USD plus shipping from lithia toyota, http://www.lithiatoyotaparts.com/parts/index.cfm?searchText=8942220010&make=Toyota&action=oePartSearch&siteid=215542).  It seems to be the same part for many toyotas tho so perhaps pick-a-part might be a cheaper option.
 

Checked your map sensor? or are these AFM?
tried some injector cleaner, use the toyota stuff, very very good, but over do it, will kill the injectors, use it every 40,000kms had similar issue, cold starts would run rough, ran injector cleaner, fixed it, perhaps the CSI was a bit clogged? not 100% sure.
nothing as severe as your issue tho.
check the basics, plugs, leads, make sure its at correct timing, (put into base timing mode)
check coil for corrosion etc etc,
might not hurt to do a comp test, make sure you havent blown a HG as once warm it can reseal if minor.

i think the problem as others have said are in your adjustment screws tho, but wont hurt to check those things however.
depending on kms aswell, wouldnt hurt to stick a new 02 sensor in, worked wonders on mine, fuel economy was restored from 14l/100kms to about 8-11l/100kms
and power was returned. best 100$ i ever spent.

Do you have a boost/vacuum gauge?  It'd be interesting to see what your vac sits at while at idle and then while warmed up as that can usually point to a leak.  I would have thought a vac leak would be likely but again, its the same thing that gets me with mine is that if it was a leak why doesn't it have issues when warmed up.
 
When my HG went (not a minor leak) it didn't affect idle and hopefully that's not your issue. 
 
The advice I've had about mine is to try another known working AFM as the next troubleshooting step, it's the one remaining sensor (and if ECU is misreading the air temp/quantity then that'd do similar, and it could only have issues with certain temp ranges.  I just need to find someone willing to lend to test.
 
Another thing to check - cold start injector timer switch
http://www.mr2australia.com/mr2play/tm.aspx?m=64032