Mysterious engine issue, bad idle, missing, only after warm

So, I have had my tacoma for 2 years now. i have made a few mods with the suspension and audio.

The other day I noticed a significant oil leak and traced it to a few loose valve cover bolts, but I decided if i was going to get into it, I may as well replace the gaskets. I did not replace the 2 intake gaskets as i didnt think they needed to be replaced. After looking at the inside of the intake and seeing a decent amount of gunk in there I cleaned the 2 pieces as best as i could with some towels and degreaser, then after reassembly I did a seafoam treatment through the intake. i have done these treatments a dozen times on my different BMWs and have never had an issue. After the valve covers and intake clean I made a 90 mile round trip up to the snow with no issues.

The next day i went out to a little play area with my brother, this was a 20 mile trip, with about 15 miles of 4x4 in the rough and mud. on the way back home i noticed the truck running odd. at about 1/3 pedal the truck would shake and the engine wanted to die while driving 65 on the freeway. next day i started in the morning and drove for a few miles with no issue and as soon as the engine was warm it started with idle issues and the engine felt like it was missing at 1/3 pedal, less pedal and it was ok, not great, but ok, and full throttle felt ok. about 15 minutes later and it was running normal again. this morning the same behavior and timing.

A few times during the odd running behavior the CEL flashes, somestimes it flashes like 6 or 7 times and sometimes it flashes 40 times. i have not had a chance to take it in to get the computer read yet.

Any ideas what might be going on without having to go get the computer read?

 

Did you check your sparks plugs maybe one is dead usaully when the plug doesn't work the engine starts to shake alot

 

Did you hook up all the vacumm lines right and also any other things that you unhooked

 

I originally thought plugs/plug wires/coil, but i checked to make sure all was plugged in properly, I did not pull the plugs to check, they are fairly new, maybe 15k miles old, and why would a plug go from working to not working, then working again?

 

Not sure I'm just trying to give you ideas if you forgot to hook up anything

 

Yea, I am just completely stumped by the fact that it runs fine, then goes whacky for a while, then goes back to being normal again. I am planning to go to an auto parts place to see if they can run a free diagnostics scan on it after work.

 

Post once you fixed the problem this might help out anyone else who has the same problem

 

So it looks like the issue ended up being a faulty seal for the spark plug tube on cylinder 3. Oil was seeping into tube and causing the coil to shortagainst the wall rather than through the plug. CEL came back as misfire on Cylinder 3.