Hey everyone,
First time poster, long time lurker

I swapped my truck (M/T) with a 3.4 out of an 98 runner (A/T) a couple of years ago. It ran well for a while and I was really stoked on how it was preforming. Then while driving across the country some dink forgot to put my gas cap back on after filling up (I was in Oregon at the time before they changed the pump yourself law). Before this happened I was getting around 320-330 miles per tank. So on my next fill up in California I realized my cap was gone. No big deal, get a new one. But that next tank only got me about 250 miles and it has stayed that way the whole way across, even after running some Seafoam through the tank. No big deal I thought. Did the fuel filter when I got to my destination, still the problem existed. So i said screw it and went through the full fuel system because surely it needed to be gone through anyways. New fuel pump, new plugs, new wires, and got my injectors cleaned professionally. Still same issue. So then I cleaned my cat and my new o2 sensors that I put in with the swap. No change. Then I did my MAF, TPS, and coils. No change. But I started to notice a small reoccurring misfire. I had a disposable income at the time so putting new parts in wasn't much of a money issue than more of a personal issue that i was having with my fuel and power economy. Because fact was, I was loosing the newly gained power that I had gotten by putting the 3.4 in. So after sometime I asked a buddy who had the same year Runner (M/T) as my engine if I could try his ECU out to see if I can pull some codes. Sure enough I pulled two codes. One for a misfire on 2 and a knock sensor code.
So after doing the following to my truck:
New plugs, wires and all the coils
TPS, MAF, Airfilter
Fuel pump, fuel filter, injectors professionally cleaned
I checked my timing on the engine which was dead perfect, (I did the belt water pump and oil pump when I did the swap)
So then I swapped my wires around to see if the misfire would move, it didn't. I pulled the plug to see if it was wet with fuel, it was, I checked for spark, there was. So what the hell?
I'm thinking that I have a stuck valve because when I fire the truck up there is no misfire but as it warms up there is an audible misfire. To me it seems like when the engine warms up it warms this valve up and then it sticks. If the rings were bad it would make more sense that the engine would misfire right away due to lack of compression.
Is the knock sensor and this misfire related? Is there something in the timing that I am missing? I read somewhere that someones crank signal gear got misaligned and their timing was off just enough to screw up combustion on only one cylinder.
Any help would be appreciated. I'm not too afraid to rip into things to figure them out, I just don't know where to go from here.
Thanks,
Johannes

 

Perhaps insufficient valve clearance

 

So get valves adjusted? Anyone else have some insight?