A few things to test , has the cam sensor got a 5v feed or 12v feed ..if its 5 volts there was a mod to change it too 12 volts , i carnt remember where i saw it .......sum ford tech bulliten somewhere ??
Thre is a modified cam sensor for this engine, i think its only availiable from dealer , i think the modified one is grey and non modified is black
or it could be other way round (sorry to be a bit sketchy it was over a year ago )
You say you have scoped cam and crank sensor,have you another vehicle to compare waveforms with ??
Is the crankshaft sensor all the way home , on the manual gearboxes the bracket that the crank sensor bolts into is elongated it could be to far away from the trigger points on the flywheel ,it doesnt move up and down much maybe 5mm but it makes a big change in amplitude on the signal
HTH Lee
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