Dunno what to tell you about the fuel filter. Maybe resetting the ECU (disconnect negative batt. terminal for 10-15 min.) will help. For an intake, get rid of the plastic resonators by purchasing a CTA intake here...
CTA Motorsports This removes all plastic parts except for the MAF. Good investment, and the sound is incredible.
Removing the exhasut resonator is kinda iffy. Some report gains, as seen above, others report no noticable difference. The only truly consistent difference is the noise. If you really want to hear your car, go for it. If not, but still want to do it, you'd better spend some $$$ on some audio equipment.
Another alternative is to upgrade to an SVT exhaust. This is known to show small but noticable gains in powerband. Mine can be seen here:
Whatever you do, have fun.