What would cause an intermittent misfire if the sparkplugs are new?

A few months ago my car stalled while driving. We replaced the crank sensor, spark plugs, oil filter and did an oil change. About 3000 miles later my engine light came on, but it wasn't running rough or anything. The code said it was a misfire on #3. My mechanic cleared the engine light to see if it came back on and I put in some injector cleaner. The light didn't come back on so I thought everything was ok. Then, today it went on again (about 900 miles later). The only thing I noticed was that when I first turned the car on it was a little rough for about 2-3 seconds, then within 30 seconds or so the light came on. This time it is a misfire on #4. The only other thing is that sometimes the AC will cut off if I idle too long, and if the car sits without being used for a few days it may have a hard time starting (but I pump the gas a little and it smoothes out). I have a really honest and good mechanic so I know he didn't do something to intentionally mess with me, but he has retired since then and I am not sure how urgent it is to take my car in (money is really tight). My old mechanic would let me pay in installments. He gave me a referral, but a new guy might not work with me as much.