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Man, you've done just about everything to that car! Don't worry, once you figure this misfire out you will be happy with it for a long time.
My gut tells me that indeed an injector might be the problem. I don't think it would explain your horrid gas mileage unless it was leaking fuel all the time. If that's the case, you should have a plug that looks quite different from the other 5. Since you just re-did your head, I would go ahead and pull the plugs now and see what they have done since you put your head back on.
CIS injectors are funky things. They don't have a solenoid, they open and close purely by the pressure put on them. If they go leaky, a lot of things can happen. First the nozzles get cloggy with varnish and spray pattern suffers, and if they really stick open bad you get fuel pouring into the manifold. If this is happening, the evidence would be in the manifold with excessive varnish deposits. Also, if this is happening, logic would indicate that a hot-restart would be very difficult as you would lose your fuel system pressure rather quickly and you'd have a ton of fuel in the cylinder that was bad. I've even heard of hydraulic locking occurring on CIS systems with bad injectors.
An injector that is not opening properly sounds more likely when looking at your motor's guts, but that doesn't explain the mileage problem.
I went back and looked at the photos you posted when you had the head off, and I don't see any obvious signs of flooding injectors.
Maybe what you've got here is several injectors that are fouled from bad gas or from an extended period of the car sitting. If you had several injectors with poor spray pattern it could explain everything.
Have you tried running any sea foam or similar through the fuel system?
Good luck!
-tp
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