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Jenn ,The check engine light flashing means the computer is seeing a direct engine misfire on this cylinder. When you changed the coil did you also change the spark plug?
I would still try swapping the number 2 spark plugs with the number 3 spark plug and see if the misfire moves. If it dose then the spark plug is breaking down. You can do this with out having to replace any part just to see.
As I am sure you know in order for the engine to fire all cylinders you need good spark, injector pulse and good compression. If the coil is new and the engine runs on all cylinders then in most cases this type of misfire is usually caused by a failing spark plug. Swapping them over will verify if in fact that is the case. If not let me know and we can work from there if need be.
You can clear the code by disconnecting the negative battery cable for a few minutes and then drive it and see if it resets.
Okay then you are going to need to drive it for a while till the drive cycle sets.
Okay while you getting the drive cycle to set lets see if in fact the light returns and if so what code comes up.
If you where able to clear the code and your sure the spark plug as well as the coil checks okay then that only leaves checking the injector and or checking for a vacuum leak which could cause a misfire on that cylinder.
The best was to check the injector is to swap it with the injector from #1 and or #3 cylinder just like the spark plug and see if the misfire moves. To check for a vacuum leak you need carefully spray added fuse such as carb cleaner in and around the area of the #2 cylinder looking for any difference in the way the engine runs.
Okay in order for the cylinders to fire you need good spark to the spark plugs, injector pulse at the injector and proper compression. Since the misfire comes and goes and you are sure the coil and spark plug check okay thent he next step would be to check the injector by swapping this cylinder with one of the other cylinders and see if the misfire moves.