88 civic with b16a swap missing and surging

About two months ago I took my car to Mahdavi Motorsports in Atlanta. They swapped a b16a into my 88 civic hatch. They also installed a cold air intake (too small), high flow cat, DC sports header, custom piping, and a new stage 1 clutch. With high expectations I went to pick up my car. When I left it ran good for about 40 to 50 miles ( maybe less). After that it started to act funny like it was missing. I thought it might go away (ha). Now two months later the car is still missing. It spits and sputters sometimes as I'm climbing in the RPM's, then all the sudden it clears up. It seems to do this throughout the rpm range and even worse if I'm driving normal. If I gas it hard it seems to be less noticable but its still there. Its especially noticable at about 3 to 4000 RPM right before V-TEC. To try and remedy the problem I bought a fuel pressure regulator and gauge kit. I bumped the fuel up to 35 psi from about 22. It seemed a little better but not much. I'm new to imports and don't know what to do next. I was thinking about trash or rust in the fuel tank because the car set up for a while before i bought it. Or maybe its one of the sensors or something. Any help would be greatly appreciated.