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.

I kept looking for the ignition computer in your list of replacement items; I take it the ECU was the LH2.4 controller (-951 or what's the other one...).

Plugs could be black for missing spark too but I can't think of anything in the ignition system you haven't already replaced that would consistently remove spark after warm up period.

If the notch doesn't show up, it could be the vibration damper has come unglued and is no longer reporting the correct position with its notch.

Not common on cars after 88, but a fault in the wiring harness or mangled connector pin could keep the signal from your ECT from arriving at the ECU and EZ-116K ignition computer. To check you should be able to measure its resistance at the computers' plugs, pin 2 on the ignition computer and pin 13 on the fuel computer. The charts temp vs. resistance are in Bentley.

Read your post twice and I still, like you, wanna blame fuel. I hope the timimg mark not even making an appearance is just a red herring due to an unglued damper. Haven't tried it myself, but I suppose you could double check by aiming the light at the cam gear with the timing cover removed. Can't be that far off if it runs well cold. Fuel pressure could still be high if return line is blocked.
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Art Benstein near Baltimore

I bought a used ECU (I think it was the 951, I dont recall anymore because it has been months since I bought the replacement ECU). When I installed the replacement there was no change in performance.

Also I should have mentioned that I have replaced the main relay (ECU/fuel pump).

ECT=Temp Sensor?

Basic question, the higher the RPM's the more enrichment the engine needs right?
If so then perhaps the hose to the FPS is clogged causing a constant fuel pressure. Too right at low RPM and too lean at high RPM?

Thanks.

If you're in the passenger seat, the fuel ECU is the metal box to the right of your toes, the ignition ECU is the black plastic box in front of your toes. Sounds like that one is still the original, right?

Sorry about the shorthand. I think ECT abbreviates Engine Coolant Temperature, but I could be making that up. I use it to distinguish that sensor from the gauge sender like you mentioned often gets confused. In your car it has two thermistors referenced to ground, one for ignition computer and one for fuel. That is why I mentioned both pins in the previous post.

The vacuum supplied by manifold to the fuel pressure regulator allows it to reference the manifold pressure instead of the atmospheric pressure, because that is where the fuel is squirting. So the net result is constant fuel pressure relative to the inside of the manifold. I doubt your vacuum hose there is clogged, but it should be easy enough to pull it off and feel the vacuum.

The rpm enrichment is done by the fuel computer increasing the duty cycle of the injector opening.
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Art Benstein near Baltimore

Yes, the EZK116 ignition unit is still the original one.