Hello Sdhesseltine.
The flashing check engine light is telling you the engine is misfiring and your description of the problem confirms that.
There will be a code stored in the vehicles engine computer that will tell you which cylinder(s) is/are misfiring.
Spark plugs, ignition coil, fuel injectors or internal engine problems will cause this.
If it has been a while since your last tune up it would certainly be a very good place to begin.
The usual tune up stuff, spark plugs, air and fuel filters for the basics.
A fuel filter will not be at fault in this case but is part of a tune up on this model.
If you require further advise, please ask me here in comments, be glad to help.
Thank you for using FixYa.
KL
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