Don't bow to my experience, I don't have much, but what I have learnt over the years is that sometimes it's just basic knowledge, logic and common sense you need. Because one will always feel inadequate because you are not experienced enough, people sometimes overthink a basic issue and think it's something complicated.
You said your pump checks out and pressure was tested, injectors replaced as well as the fuel relay, so let's have confidence in that and assume everything is fine.
Now for the spark, start the car and when it's running you will need to remove each of the HT leads and notice how it affects the engine, sometimes the coil is working but not 100%, get gloves some properly insulated plier for this, they are not called high tension leads for nothing.
You will have to rule everything out on the spark issue all the way to the soak plug itself. I just hope your guy did not do some funny bridging stuff on the wires that only himself understands.
Go through all the sensors and check if there are no corroded or cut wires, sometime LS it happens that with bad handling some of the wires snaps.
Check the vacuum hoses for cracks, there must be something, there can't be a mystery of a car that was working fine the previous day and all of a sudden there's a baffling issue that cannot be solved. Do that ecu resetting thing suggested. If everything fails then it's time to look for an expert.