have you replaced the spark plugs with a decent set of tripple probes, perhaps they are sparking at the wrong time?
It might be worth swapping the ECU, it may have been remapped for a different engine and swapped on at some point. Also, maybe the injectors are faulty, or have been replaced with a set of the wrong rating dumping too much fuel in...
Might be worth getting the pressure at the fuel rail checked also, perhaps a blockage in the return is holding the pressure up too much? There is a bolt in the end of the fuel rail, if you remove it you can attach a pressure guage there
