running lean?

i recently had some issues with my 01 SPI SOHC engine idleing rough, it was suggested that i change the spark plugs and wire. I did this and it made a big diffrence, but did not compleatly fix the issue. The other day i was driving home 1hr drive over a 20min pass(mountain). When i got close to home on the flat i noticed my check engine light on. OH CRAP. I went to the shop today and they ran the scan test on it, and it gave an error code of running lean(double crap). They suggested changing the fuel filter, so i had that done. After that we talked and basicly came down to their not 100% what is causing it, gave me a few things like could be a fuel pump, faulty sensor, or 2 worse case of head gasket i beleive they said or the ECU(now iam really worried) The guy told me that the car has to go through a "drive cycle" and if the light doesnt dissaper in a week say, to call in and then they want to do some other tests. The test he was thinkin of was to clean up the engine look for any leaks, and a smoke test for a possible vacume leak. And then go from their.

Question is does this sound avisable? or make sense i really dont know much about this to tell the truth. Guy was great though charged me only for scan test and filter.