1998 Plymouth Voyager Occassional rough running

I have a 3.0 98 Voyager, and drive it 150-220 Miles per day. It gets turn off an on 25-30 times per day as I make frequent stops. The issue is for about 10-15 minutes per day, usually twice per day, the van runs just like it has bad plugs wires etc, or a bad fuel filter. I have given it a complete tune-up as well I have changed the fuel filter. It still happens. No check engine lights ever come on, thevan does not stall, just runs terrible. It happens while at normal driving speeds of 50-60 MPH, and maintains that speed while running so poorly. Really can't tell if it affects my fuel mileage at all. The only kind of constant I have noticed is at the end of the day when I refill my gas, it happens more often on the way home, which is about a 20 mile drive from the gas station. Any thoughts.