No spark on 2 or 4, but good coil pack?

04 Aveo was running bad. Ran seafoam, changed, plugs, changed wires. No significant improvement. Checked battery, it was bad. Left disconnected for hours while I got a new one so I could force computer reset. Connected the new battery and it sounds MUCH worse. Put a timing light on plug wires to find that I've got no park on cyl 2 or 4. Can't believe it even runs, but sure enough, I can pull those 2 and change nothing. Stole the coil pack from my 05 to verify it was the pack, and no change. replaced coil pack on 05, it still runs fine, and the timing light registered spark on all 4 cyl. back to the 04. Put a brand new plug on a tested wire and held to ground on battery. I can see a pathetic small spark, but the timing light doesn't register it. Not sure how that can even happen.
So I'm pretty much down to wiring harness or ECM right? I'm assuming I can't test ECM by stealing the one from my 05 which is a manual when the 04 is automatic.

Any suggestions or thoughts on this?

The ECM coil driving process pairs 1/4 and 2/3, which makes it less likely (but not impossible) for the computer to be bad. Have you swapped ignition wires around, just to confirm they are good? (yes, I read they're new).

Assuming those wires are good, then a another thing that can be tested are the ECM ground signals going to the coil. Those signals for cylinders 1, 2, 3, 4 are at ECM pins M35, M33, M1, and M51 respectively.

One thing to keep in mind is that the ECM will shut down fuel and spark to cylinders if it detects severe misfire (which could be caused by many different things). Not saying that's the case with your vehicle, but it needs to be kept in the mix, until the actual cause is diagnosed.