Multiple Cylinder Misfire Detected

How long have you owned this car?

It's probably a bad head gasket. When the engine is cold, remove spark plugs, pressurize the cooling system, and use a borescope to look in the cylinders. Many threads in this forum with information and pictures of the cylinders. Do a search to find them.

 

Yeah trust your gut.

Take a look at my signature: there's a couple of links related to head gasket repair, and the full engine section from Repair Manual is the bottom link. (on a phone turn it landscape to see signatures)

Has the EGR system ever had the carbon accumulations cleaned? My 2 cents, this should be done every 50k miles.

 

It's probably a head gasket issue. You can verify by borrowing a bore scope from your friendly auto parts store. Remove the spark plugs to look at the top of your pistons. there should be a black carbon layer across the top - if not it's been steam cleaned by the coolant leaking into those cylinders. You can compare it to 3 & 4, all 4 should be uniform in color and consistency. You could have an injector issue, but 1 & 2 is usually where they blow. You need to pressure test the cooling system when the car is stone cold. When the engine warms up, it expands and seals the leak. That's why people who get the early morning misfires know that their head gasket is leaking.
Running the car like that increases the chances that you may warp the head or engine. Make sure you replace the stretch bolts, when the head gasket gets done. Also take the oppuntunituy to clean out the EGR system and replace the valve guide seals.

 

Not sure if I've linked it elsewhere, but the attached TSB (for oil consumption remediation) has part no's for Toyota's:

gasket kit (has head gasket, plus most every other gasket, seal and o-ring you'll encounter)
head bolts

Also, top two links in my signature have EGR cleaning tips/info.