An O2 sensor problem will usually cause a CE light, but the exhaust mods you mention shouldn't effect your O2 sensors. The O2 sensors will not affect starting your engine, so I would suspect some other problem. (Ignition, fuel filter etc.) It sounds like you have a custom intake, so maybe there is a leak or something going on there?? What type of engine, mileage, and other mods do you have? Any other symptoms?