95 Fuel Filter

My car starts up right away and runs fine for about 3 minutes and runs good driving then the longer the car is on the car spudders horribly, it will do a jerking motion while in gear just to go faster, when in 4th gear you can floor it and it will go slower. This engine is a d16z6 with 54,000 miles, new spark plugs, clean gas, I cleaned the throttle body with some cleaner. The mechanic said my check engine light said i needed a new ecu, I looked at mine and it was fried then I replaced it with a new one and still has the same problem, I'm thinking it's the fuel filter, what do you think?