I didn't see any description of the mechanical condition of your engine. Have you done a compression test and a cylinder leak down test?

Are you burning any oil or have smoke emitting from the exhaust?

I really think you have to first determine the mechanical condition of the engine before looking into the controls.

If the engine is sound, then electrical test of the controls would be the first order in determining if they are contributing to the problem. From the sensors you should then determine the condition of the wiring to the ECU and the electronic ignition control. If there is continuity and the resistance (ohms) are within specification you should then determine the condition of the ECU. It could very well be that the controls and wiring are fine, but the ECU isn't functioning properly and has to be re-programmed. If within specification and/or current software updates the final place I would look is the performance of the transmission. Sorry to have to bring up these basic items, but when all else fails remember its back to basics!