Did you check your relays and fuses? My old car burnt the main engine relay, but it would just barely complete the circuit, so the car would run but mysteriously would just randomly run like crap, then stall out then start back up. I tried timing, new plugs, wires, cap, rotor, and new censors. I finally checked voltage to my fuse box, then to all of my relays and noticed the voltage would fluctuate really bad on the main engine relay, changed it with a new relay, never had the problem again. Just a thought.
Also how much have you tweaked the stock ecu tables? have you tried setting them back to stock? Or have you loaded the cobra tables in it yet?