Ok, just throwing this out there but try a can of SeaFoam. When I bought my car it also had a misfire (just barely noticeable by shaking/vibrations but it did cause the light to flash) and I ran a can of SeaFoam through the gas tank and it magically went away....for a while. After that I had a spark plug wire go bad (at 159,000 miles it was time for them though) but after a can of SeaFoam and plug wires mine runs as strong as ever.
The SeaFoam treatment can't be easier either. I got a can at WalMart for $7 and there's instructions on the back of the can. All the stuff does is clean certain parts of your engine...in my case I probably had a dirty fuel injector. It's simple to use too, just dump the stuff in the gas tank and forget it. Be sure to read the can though as there are recommendations on how much to use based on how full your gas tank is at the time.
Might not cure it but for $7 I'd give it a shot.
