Don't know if this is related, but my last car did this for about 4 months and then out of the blue the crankshaft broke.
I had the car in the mechanic about a month before it happened. They could not find anything wrong.
I took the exact same steps as you (plugs, fuel filter, basically new ignition system). Nothing helped, but I was able to lighten my wallet.
I'm not bitter about it, though...If it hadn't happened, I wouldn't have bought the Contour!

I hope you aren't going to need a whole new engine!

Ride: 2000 T-red SE
Beats: Kenwood 316S, Alpine MRF200, Orion XTR 6.2, Coustic 400SE
Mods: CTA, Magnaflow exhaust, SVT Instrument cluster, Knuaberized doors, side markers, F***ed up painted headlights.