2002 Malibu died while driving, now wont start

I know you get this question a lot.
My sons car died while he was driving and wont start since. I'll just diarrhea
out every thing that could possibly be pertinent.
We replaced the motor about 5 months ago, He overheated the previous
one. We've had no problems since, purrs like a kitten(normally).
He said the Oil pressure light, water level light and battery light came on right
before or as it died. We tested voltage, jumped it and replaced battery with a
good one. All the pulleys turn when you start the car and it coughs the first
crank every so often, but other than that it doesn't sound like there is any
ignition.
As well, when you sniff at the vent right before the throttle body there is no
gas smell.(Not sure if that's  good test :) )  We confirmed spark on one
cylinder(ignition coil was tested as good at motor swap) and pressed the
bleed valve on the fuel rail and got a squirt of fuel. All fuses are good.
The theft light is on when the key is turned to on, but i don't know that that
isn't always that way, for example the battery light and oil light come on while
it sits there with the key on.

I thought it was gonna be a quick alternator swap, apparently not. Any
assistance appreciated. He is borrowing my car in the meantime :(