Have Toyota Questions? Ask a Mechanic for Answers ASAP
If the check engine light is coming there has to be some kind of code set in the system. Did O'Reillys have a proper scan tool to plug-in to the port under the instrument panel or were they under the hood at that port?
Do you have access to another scan tool or do you have a voltmeter to run some diagnostic tests and checks? Or are you just looking for general ideas as to what could be going on?
Do you have any history on the vehicle leading up to this current problem? At this present time the vehicles in a no start condition correct? When you turn the key to the on position does the yellow check engine light stay illuminated? We need to know whether or not you can read codes or does it still say not communicating. I can recommend a good generic scan tool for about $60 if you would like I recommend everybody have one it will save you hundreds of dollars in diagnostic fees. If the vehicle is not currently running you cannot get it to O'Reilly's to have them check for codes.
The mass airflow sensor rarely fails and depending on the mileage a fuel filter typically won't cause this type of problem with no communication and cylinder misfire.
No it is not good for the catalytic converter especially if the check engine light is starting to flash this means there is cylinder misfire and it will damage the catalytic converter. You need to get a scan tool so that you can operate while the problem is occurring. Click or copy and paste this link for a good scan tool that I recommend everybody have. If you cannot get one you're going to need to find out why it is misfiring typically this is due to a bad ignition or possibly spark plugs. The description of the not starting sounds like possibly an injector that is leaking the only way to know this for sure would be to do in injector leak down test or after letting it set pull the spark plugs out it the spark plugs are wet or carbon fouled black. Excessive ethanol content will also cause this problem but typically it will not smell like raw fuel once it started. Based on the odor that you're getting it sounds like you may have a couple injectors leaking. You could try some injection clearing the tank that may help.