If it's hiccupping, have you checked the plugs and wires lately? Maybe the "hiccups" are really misfires. My '98 Contour needed plugs/wires at 35K miles while my '97 Mystique just keeps smoothly firing with the originals as it approaches 60K miles. Go figure!
If you put injector cleaner in the tank, I suggest taking it on a long expressway drive so the engine gets hot and the gas with the cleaner in it is running thru the engine at a continuous high rate for a period of time. Aggressive stop-and go driving really will not get the injectors as clean as a sustained high speed drive.
Finally, yes, change the fuel filter after using the cleaner. The cleaner tends to "scour" everything in the fuel system and will probably result in additional "junk" being taken out of the system in back of the filter and getting trapped in it as the fuel passes thru.
Good luck.
