I'm betting on the wiring harness.

While a bad coil or fouled plugs will cause some intermittent missing and some performance loss, a bad wiring harness will create the sort of havoc you are experiencing.

Mine acted just as weird until the harness was replaced.

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2009 ML350 (106K) - Family vehicle
2001 CLK430 Cabriolet (80K) - Wife's car
2005 BMW 645CI (138K) - My daily driver
2016 Mustang (32K) - Daughter's car