I believe there is a pressure test port on the fuel rail, you could hook up a pressure gauge and see if you aren't getting enough fuel pressure. What brand fuel filter did you use? if fuel pressure is low at the rail (below 35-40psi if I'm correct) then either that filter/regulator is bad or the fuel pump is going out.
My Jeep: 2001 Grand Cherokee Limited, 245/65R17 Falken Rocky Mountain ATS, K&N drop in air filter, Bilstein HD's. De-badged, eagle-eye LED Tails & LED 3rd brake light, Addco front and rear sway bars, Superchips tuned & TM snip, interior 6k LED's, Gen3 ccfl projectors with Volt 6k HID lows, akebono brake upgrade with R1 Concepts premium rotors.