Engine management

I;ve got a focus tddi endura -year 2000,got smoke coming from exhaust(grey) runs a bit rough and theres a kinda knocking seemingly coming from the top left hand side of the engine,like a valve not
returning properly,ive removed and stripped down the head,decoked and cleaned it all up new valve seals the lot,but the problems still there :(
my engine management light comes on when i start the car but goes off straight away,surely this light should come on and stay on if theres a fault?? any ideas how this management system works,has a fault occured in the sensors or summat????
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That MIL behaviour is normal, and as far as the ecu is concerned there is no fault.
Tim.
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