PSA: If you're running into issues like the misfires during startup that nothing seems to change, it might not be a headgasket.
REPLACE YOUR INJECTOR ON THE MISFIRING CYLINDER.
I was on the Tacoma forums and happened across a thread where someone mentioned that apparently the coolant jacket is a bit thin near cylinders 4 and 6 in the older models, and that this (when coolant temps run hot once or twice due to other cooling system issues) causes the injector(s) on 4 or 6 to fail and then leak into the cylinder(s) when the vehicle is turned off for an extended period of time. This then floods the car when it starts up and makes that cylinder misfire.
I had been getting a P0304 code *every* time I started my 4Runner after it sat for more than an hour for at least the last month. Maybe 2 months. I tried everything short of replacing the injectors (swapped plugs, coils, cleaned everything in the intake tract). Finally took it to a shop and they looked it over and told me everything seemed fine with no signs of a headgasket failure. Yet it continued to misfire (they claimed it didn't miss for them - I think they just didn't want to mess with it any more, as it missed as soon as I started it the next morning).
I came across the Tacoma forum thread (which I haven't been able to find a second time...but will keep searching for) and he mentioned that the failed injector will also cause gas to leak past the piston rings into the oil. So, I checked my oil and sure enough, it smelled like a gas pump. Changed the oil and dove into changing the injectors (which was a hassle, those boogers enjoy making vacuum leaks if they're not seated perfectly with zero dirt. Also, don't buy eBay remanufactured injectors. They suck, and I ended up putting all of my originals back in except for cylinder #4. It got one of the eBay ones that I confirmed worked properly).
I changed the #4 injector last Thursday and after 400 miles and probably 10 cold starts, haven't had a single startup (or otherwise) misfire. I'll update if I get another CEL from them, but so far so good! Check those injectors people! They're not as bulletproof as some claim.
Edit: Found the Tacomaworld thread!
1GR-FE's, Fuel Injectors... Discoveries... | Tacoma World
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'04 4Runner -
Build Thread | '05 CBR 600RR & 1000RR - The slow vehicles ;)