2002 Ford Mustang Troubleshooting P0351

I have had no previous problems with my car for the past 4 years. On 11-24-08 I took my car to a shop & was informed with P0300 (Random Misfire). They replaced my ignition coil because my car was not picking up while driving uphill. The car ran fine for 3 weeks 2 days until it started cutting off completely. On 12-11-08 I was warming up the engine and it cut off & again while driving it 5mph. That time it took 3 turns to power back on. It drove fine 3 miles in the am & later in the afternoon 3 miles back. In the evening while on my way to Autozone(1 1/2 miles) it turned off & while restarting, the engine check light came on. I had to chug along to the entrance because it started shaking. Autozone performed the engine check & read 3x P0351 (Ignition coil). Autozone told me that it could have been a defective ignition coil & for me to replace it with another. I called the shop & they stated that it was not the ignition coil & that it must be "several" other things. I have not checked or changed out my air filter in the past 8 months What could possibly be the problem? Do I have the right to tell the shop to replace it with another coil since it has 1 year warranty even though they are telling me it is not?