I have an 1989 240 with an LH2.4 FI and EZK116 ignition, the car starts and runs fine when cold. But once it reaches operating temprature the car will stall and knock if throttle is applied abruptly while driving.
The car runs rich though, I pulled the plugs and they are dark.

I have replaced:
O2 sensor (Bosch)
Air Flow Sensor (had the old and replacement unit tested, they both check out fine)
Replaced the timing/crank sensor with a Volvo unit.
Changed the belt and checked the lineup marks numerous times.
Replaced the Fuel Pressure Regulator with a Volvo unit.
Replaced the temprature sensor (not the sender to the gauge, as might mistakenly)
Replaced the ECU.

I ran a systems diagnostics check with the module at the front left shock tower, it gives a signal that tells me 'Faulty or missing ignition signal'. I think the signal is 1-2-1, I dont recall the number but I remember what the meaning was.
I checked the timing numerous times, checking the rotor alignment on the distributor with the the notch on the housing and the timing belt, if they all lined up.

Now, I checked the timing with the timing light and it the notch doesnt show up.
Can this have any affect on the timing?
When cold the car runs fine when it is warm dark smoke will come out of the exhaust which leads me to believe it is rich. But when driving the engine will knock as if it is too lean. Maybe something is wrong with the fuel regulating mechanism. Now that I think about it maybe the vacum from the hose to the Fuel Pressure Regulator is clogged? But if that where the case the engine wouldnt knock *and* run rich. At the risk of sounding extremly redundant, the knocking only occurs when accelerating, at cruise it doesnt knock or atleast not noticably. I dont think it is the knock sensor, if it where the mixture wouldnt be rich.