First off, you should get it scanned. Plugs/wires and fuel filter are a good start and a great idea, since the 100k mi tune-up is B.S. anyway. I would start there with the simple stuff, and then move into the more daunting of tasks (fuel pressure, sensors, filters). Good luck and let us know if anything new comes up!
Sean


'99 Silver SVT Contour (2000 miles since June, now needs new front brakes and bearings) '98 CBR900RR Again (Put away for the winter)