Flashing CEL means "danger" possible engine damage may occur, this is usually from a bad misfire detected by computer.
While there are no "good" misfires, there are ones that are worse.
Computer reads the crankshafts spinning by a "tone wheel" on the crank behind main pulley.
A circle has 360deg, tone wheel has 36 teeth, so 1 tooth = 10deg, one tooth is removed, this missing tooth passes by the CKP(crank position) sensor when #1 piston is at TDC.
Computer watches crank speed by timing the 10deg teeth as they pass by.
Computer has two ways to see misfires.
1. spark feed back, when coil fires there is an electrical feed back in the circuit if the spark plug doesn't fire, a miss but not a very bad miss.
Unless there are several feed backs in a row.
2. crank speed, computer watches crank speed, when a cylinder fires it adds spin to the crank, when it misfires it doesn't, this doesn't slow the crank down but doesn't speed it up either, so a miss but not a bad one.
Spark always happens AFTER piston passes top dead center, even though spark timing may be 10deg BEFORE TDC, by the time the spark plug ignites the air/fuel mix enough to push against the piston it is passed TDC, if it wasn't then it would SLOW the piston down and the crank, this would be a bad misfire.
And you would get flashing CEL.
I would check coil pack firing order, and make sure spark plug wires go to the intended cylinders.
Then unplug the Intake side coil, the 3 wire connector.
Now start engine, if it has a miss then firing order is wrong or bad plug or wire.
On the 4clyl Lima engines only the exhaust side coil and spark plugs work when starting.
Intake side will start to work after engine RPMs are above 400.
If engine starts and seems to run OK with just the exhaust side connected then problem is most likely on the intake side spark.
CEL will come on with coil pack unhooked, that is normal.
You do need to have the codes checked, it could be the cam sensor and crank sensor are not in sync.
The Flashing CEL is a "get it looked at right away" thing, CEL just being on means "have a look when you can".