I had the same problem with my 03 GT turbo. The pcm was replaced by the dealer, but the miss was still there. I replaced the OEM plug wires with Bosch Premium wires guarenteed for life and changed from stock plugs to single platinium champions. Later when the Iridium NGK's were available I went with heat range 6, which seemed perfect. The OEM Champion plugs I removed had missing ceramic around the electrode which was causing the miss or drop out. I have had the NGK Iridiums for nearly 20k miles and still she has a smooth idle.You may have a combination of problems, the PCM, plug wires and good plugs.I also saw the Champion plugs were leaking that was exibited by the carbon tracing from the metal body up vertically over the ceramic insulator. Both the OEM and single platinum plugs showed this characteristic, I will only use NGK (LZTR6AIX-13) gapped at .045 which never showed any sign of leakage. The use of the std Champion OEM plugs in the turbo can cause engine damage as the ceramic breaks away and falls into the engine and does nasty things before it passes the exhaust valve and goes thru the turbo.
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