I think your injector signal may not be going low enough to be consistently recognized as a low by the MPU. When looking at signal levels on my 91 CRX HF the signal was only dropping to about 1 volt for low which the MPU logic levels still register as a high.
Try adding a resistor in parallel with the Zener diode to create an input voltage divider. Try a resistor of about 1/4 the value of the input series resistor.
Mike
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