Violent Engine vibration on colt start- instantly stops after ~30 seconds

Hi all, I have a 1999 4runner with the 3.4L v6, 5 speed manual, 235k miles. 
 

I have, twice over the past ~50 cold starts had an odd phenomenon pop up. 
 

I will start the car for the first time in the day and it violently shakes- like I'm thinking all the engine mounts broke overnight. I'll shut it off, start it once or twice more real quick, still shakes, so I'll pull out of my space and try to drive through it. Both times it has instantly smoothed out (like a switch is flipped from "shake" to "smooth") after approximately 30 seconds of run time. It runs perfectly afterwards, no lasting effect. 
 

There are no codes, and here is the recent list of engine/fuel systems maintenance, and reasons why I did them:

Spark plugs/wires (reason: regular maintenance)

new Idle air control valve/cleaned  throttle body (reason: to fix inconsistent idle ~2k miles ago. Seems to have fixed the issue)

Aftermarket intake (reason: boy racer)

new fuel filter (reason: regular maintenance, and I believe one of the 2 shake instances happened prior to this). 
 

seafoam to top end, crankcase, and fuel tank (reason: unsure of prior engine maintenance, and top end looks very gunked up upon looking into oil fill hole). I did this one and it ran like crap until I burned everything out. This was ~1000 miles ago. 
 

Any advice on where to start? I'm thinking clogged fuel injector, like something was dislodged past the fuel filter. I've had a boat engine do this before. 
thanks in advance! I'm at my girlfriend's this weekend, so troubleshooting will not be happening ASAP, but I need to know where to start! 

It's almost like a severe false air leak that makes it run poorly until the engine goes into closed loop fuel control.

Hmm. I'll be honest I'm rather new to diagnosing problems (I'm an adequate parts changer though!), so I had to read about that issue. 
 

seems to me that would present a consistent problem, would it not? 
 

the inconsistency is what is killing me 

It sounds like a leaking fuel injector. It floods the cylinder and clears up once that cylinder starts firing. 

Boost_Crazy said:

It sounds like a leaking fuel injector. It floods the cylinder and clears up once that cylinder starts firing. 

+1

Both decent ideas.  A scan tool will help figure out whether it straightens up as it goes to closed loop, or whether it's counting misfires on a particular cylinder.  If it's intermittent, I like the leaky injector.  A leaky head gasket will do the same thing, but would probably be pretty consistent. The tailpipe would smell like burning antifreeze as it was cleaning up from it's misfire.

Hmm, leaky injector makes some sense.
 

Looking at diagnosing- what would I be looking for with my obd2? Seems like if it takes all night to sometimes show up (aka leak enough?) I wouldn't be getting any codes, right? There are none on the dash at least. 
I will certainly plug mine in when I get home -it's a cheap Amazon version, I'll see what it shows!
Would pulling the plugs show a miscolored plug so that I could verify which injector? 

Your biggest aggravation will be the random nature of the problem. You would need to have a good enough tool to show which cylinder is misfiring in the live data, then pull that plug and see whether it's wet with gas.

Yeah that is going to be a pain. 

I'm going to start looking for a better scan tool. One with live data like the UltraGauge. 
 

thanks guys, I'll be back with more info when I can get to my tool! 

Ok, got a little further into this. Still extremely inconsistent as to when it's happening, but pulled out a code reader. Still no codes (in case the dash light was not being signaled), and my plugs look like this: 

they all look the same, so that's good at least. 
Any suggestions as to how to proceed? 
I'm thinking have it sit a full day and pull the plugs to see if there is fuel in the cylinders, but that's all I've got! 

...Is the violent shaking accompanied by loud rushing-air noises?

A fan clutch that seizes then frees up can do some wild things sometimes...