You definately need to check for spark.
Get a wiring diagram to help (library)
Pull a sparkplug and see if it's wet from fuel.
The pumps will not run if the engine is not running, but as you know you can bypass this.
Turn on the pumps and crank the engine (I'd check for spark first), if it fires then it could be a weak ignition or low fuel pressure or volume, plugged filter.
The ECU requires a signal from the coil to keep the relay on and the pumps running (it will run about 1-2 seconds after the engine stops).
You can check for coil signal at the ECU and ECU output to the relays and injectors. Can you here the injectors operating, maybe not when cranking, probably have to check for a signal on them.
Don't condemn the ECU without checking everything else, it's pretty tough.
BTW if the ECU is bad I'd like to take a look at it, let me know.........
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744-16v,745-16v,242Turbo.245DLT