Whenever the programmer resets like that, it's nearly always an indication that the battery voltage is dropping below 9 volts when cranking. The odd thing is that you can have a weak cell in the battery and still be able to crank, but the voltage will drop pretty low. The PCM can handle voltages down to about 8 volts before it has trouble running the engine, but by the time you get that low the engine won't crank anyway so it doesn't matter. I'd seriously give the battery another look.
I don't have any explanation as to the "knocking" you're experiencing, especially if your PCM was already programmed back to stock. It's very possible that the cam phasers were making some noise. They like to rattle a bit until the oil pressure comes up. How cold was it when you started this morning? Temps may be playing a factor in both issues.
Let me know.
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Bill Cohron - The Mad Doctor  
Power Hungry Performance - The ORIGINAL in Ford performance tuning... Since 1997!
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