2005 Saturn Ion misfires in clyinder's one and four

Misfires can be caused by worn or fouled spark plugs, a weak spark (weak coil, bad spark plug wire), loss of compression, vacuum leaks, anything that causes an unusually lean fuel mixture (lean misfire), an EGR valve that is stuck open, dirty fuel injectors, low fuel pressure, or even bad fuel.

A misfire in a specific cylinder should lead you to check the spark plug, fuel injector and compression.

You could try this. Here is a bulletin for this problem. Subject: SES Light and Severe Engine Misfire on Cylinders 1 and 4 or Cylinders 2 and 3 Models: 2002-2005 Chevrolet Cavalier

2005-2006 Chevrolet Cobalt

2006-2006 Chevrolet HHR

2004-2006 Chevrolet Malibu

2004-2005 Chevrolet Malibu Classic

2002-2004 Oldsmobile Alero

2007 Pontiac G5

2002-2005 Pontiac Grand Am

2005-2006 Pontiac Pursuit (Canada Only)

2002-2005 Pontiac Sunfire

2003-2006 Saturn Ion

2004-2005 Saturn L Series

2002-2006 Saturn Vue

with 2.2L Engine (VIN D or F - RPO L61
Some customers may comment on a severe engine misfire and a SES Light. Upon inspection, DTCs P0300 - P0304 may be found due to misfires on cylinders 1 and 4 or cylinders 2 and 3. If this concern is encountered, inspect circuits 406 (IC Control for 2/3 Coil) and 423 (IC Control for 1/4 Coil) for an intermittent short to ground or poor connection on either end. Depending on the model, these circuits may short on the AC lines near the AC compressor, on the transmission mount, or on the transmission lines where they enter the transmission. If there is no problem found with these circuits, inspect the ignition control module ground to ensure that it is clean and tight.

If there is no problem found after performing the suggestions above and the SI diagnostics lead to ignition module replacement, replace the ignition module as directed but also replace all of the spark plugs and clean the ignition module ground to possibly prevent future ignition module damage.

This might help