As the title states my wifes RX-8 develops a "dead" miss after it reaches full operating temp. I changed plugs, wires, and coils. The coils seem to prolong the problem a little bit but it still does it. If I were going to describe it, I would say it sounds like you pulled just one plug wire off a v-6. Once it starts doing it it does it all the time from an idle all the way to redline, under load, no load. Maybe a fuel injector? I am at wits end with this car. It is on its second motor this one only has about 35k on it. We run premium gas and oil is changed regularly.

 

I'd say there's a seal sticking so you have lost compression in one face of the rotor. Try a compression check, even with your finger with the plugs out, just to make sure there's even pressure when it's turning over.
I'm not sure if it's possible, but if the crank angle sensor was going bad, or a tooth on the sensor was corroding off, there may be a miss if the signal is going away once in a while... seems like a long shot though.

What died on the first engine, and at what mileage?