I should have figured from your other tests that you actually saw spark and ruled that out, there are people that buy new ignition components and take it for granted that they are working. The fact that there is spark at all means the PCM is getting information it thinks is plausible from the crank position sensor, but it might be off enough to prevent running. One other thing I thought of is that o2 sensor is probably fine, they don't start working or influence AFR until they get hot and it takes a couple minutes of running, it'll read 0V until then.
It sounds like all 3 elements of a running engine are there and just not in sync somehow. If you did the compression tests with the throttle wide open, you effectively bypassed the idle air control valve and if that were stuck closed it might prevent the engine from firing. I'm just spitballing, you probably tried to start the car with a little throttle for good luck. The IAC could get sticky though depending how long the engine sat for.
Try unplugging the MAF sensor once, I've got a periodic no start problem in the winter and unplugging the sensor for starting has solved it in the past.
The fact that you had it running briefly on 3 cylinders makes me think there's nothing weird about the tune preventing it from running.
There are a lot of people here smarter than me that might have different ideas.