Is a very odd one......without a code this ones going to give you headaches it sounds.....if you had a labscope/meter to see the waveform of the cam and crank signals to see if there is a issue with them or the wiring.....one thing im thinking to check is to check your 5 volt refrence voltage to your sensors while cranking and running and see if your losing it,can check it at the coils as well as at the TPS one and two and at the MAF sensor,maybe is a bad sensor pulling tour refrence voltage down....just a wild guess but worth looking at

One other thing....what condition is the battery in? Is the charging voltage ok? Wondering if maybe there is a bad diode in the alternator causing to much AC voltage into the system......can put your meter on the alternator post at the alternator and set meter to measure AC and should be less that.5 v i believe.....might be less than.3 is the prefered cnat remeber off hand..