I've read a LOT of threads about misfires. I haven't seen this problem before, so here you go.
I had a bad misfire on #3. I ohm tested the injector, and it was out of spec, so I ordered a new set of injectors and pulled my plenum. What follows is my log of what I found. If you have a bad misfire and you have spark AND good injectors, perhaps this could be your problem also.
...So, my car is back together and running smoothly again. Actually, she's never been this smooth as long as I've had her... I suspect she's been misfiring (or occasionally misfiring, or even partially misfiring) for a long time, and I just hadn't noticed how bad it was. I'll get to that at the end.
So... I got three injectors popped back out of a bad rail, re-oiled, and popped back into the replacement rail. (see the original thread for that story!) Installed the 5 new rail seals, bolted down the fuel rail with a span on new gates fuel line between them, and started buttoning up the engine. Plenum back on, wiring back together, everything. I took my time to get all the wires right, all the vacuum lines on, and I was ready to test.
To relieve the fuel line, I just pulled the fusible link for the fuel pump next to the battery. It really is the easiest way to do it. After reassembly, I replaced the fusible link, put the key in and let the fuel pump pressurize the line. I found a leak at filter because I forgot to tighten those clamps. I fixed that, and was ready for first start.
She started up pretty easy after 10-20 seconds of cranking (I assume the fuel line needed to purge air). Once she was up and running, ... wait.. she's still missing. @$##^%#$^%@$#% Arrrggg!!! I pulled the coil on #3, the cylinder that was missing previously, and yup... no change. So that cylinder was still dead. I was PISSED. I have spark, I have new injectors all around... I feared the worst, that maybe the compression on that cylinder was low... oh god... nooooo...
I decided I needed to prove the injector was getting a signal from the ECU, and so I went to my computer to research... Found this thread, and decided I was going to have to try this CAS trick with a 12v LED stuffed into the #3 injector connector to check signal to the injector. It was midnight. I walked out to the garage to look a the timing belt cover to see how hard it was going to be to ... wait.. what is that... on the floor... OMG NO.. NO.. NOooooooooooooo
Ok, did you catch the foreshadowing? It wasn't a typo. I said above that I had installed the fuel rail seals, all 5 of them... wait.. there's supposed to be 6.
WTF. I just found one on the floor. a brand new one. how the @#$% did this get out of the engine?? I was sooo careful putting the fuel rail back in, I was sure I had all 6 seals in place. Obviously, I had dropped one. I even inspected with a flashlight after installing, but somehow I missed one. Now I'm REALLY pissed. It was midnight, so I went to bed.I woke up at 5 am unable to get it out of my head. I got out of bed, coveralls on, in the garage, cleaned away the debris from the night before, and was wrenching by 6. By 9am, I had the plenum back off and was down to the fuel rail again. (YES, YOU TOTALLY SHOULD DO THE TB WATER BYPASS. It's not even a question.) You've GOT to be kidding me. It's #3. The cylinder that started all this @#$% is the one that lost it's seal. 2 minutes later and the seal was back in place, and the plenum ready to go back on. I found one more fascinating fact... The plenum gasket showed a little wetness at the edge of the tube going to #3. Gas? yup. It seems that with the seal missing, the vacuum leak AT the injector actually causes the fuel spray to get sucked back up into the plenum and down into other cylinders. Holy crap. That totally explains the misfire, even with perfect spark and fuel.
3 hours later, and I'm ready to turn the key. (Did I mention that you should totally do the TB water bypass? I feel I should mention how easy it makes things...) Fuel pressure test and leak check, and ready to start the engine. She starts up. Firing on all 6. OMG. That was it. A missing rail seal causes a misfire. She's purring. I'm smiling... and I get curious.
When I took out the old seals, they looked like @#$%. Torn, cracked, split. I think that may be where the misfire started to begin with. Have a look - these are my old seals. Knowing what I know now, I suspect that these could be the source of mystery misfires for all of us. Have you checked yours lately?
Moral of the story - If you have a mysterious dead cylinder, and you pull your plenum, Check your rail seals.
I hope this helps somebody!