engine light flashes

I recently bought a 2001 ford Taurus that was involved in a wreck. I replaced most of the front end (radiator, condenser, fans, grill, bumper, headlights, O2 sensor by manifold, power steering pump pulley, and also the fuel pump which I believe was a coincidence that had burned out. I was able to start the car and test drove it. All seemed ok with a little "shuddering" which I attributed to old fuel that as the car had been parked for over a year, and a humming in the power steering. I added some fuel injector cleaner and some fresh gas, and I also cleaned out the power steering system and refilled with new power steering fluid. The power steering humming went away, however the shuddering continues and the check engine light flashes over 100 times. I have taken it to Autozone and they were not able pull any codes. they recommended that I change the fuel filter, so I did. I have also inspected the vacuum hoses and to my knowledge they appear to be ok. I also checked the coil pack and the spark plug wires to see if any were arcing, and they were not. My next step is to replace the spark plugs and wires, however I wanted some input to see if anyone else had any ideas. Oh by the way there are times that my heater will blow hot then as I'm driving it seems to blow cooler air even though the car temperature appears to be normal (about in the middle). At other times it will blow hot air without any discrepancies. Overall the car runs good, with the constant slight shuddering and the blinking check engine light. Any Ideas anyone???