in the '05 EPA motor they used smaller valves and a super "E" carb (less fuel flow). when the intake manifold was mounted to the cylinders, they put what looked like an extra metal gasket with the inside hole smaller than the manifold and the mating hole in the cylinder which basically throttled down and disrupted the flow of fuel into the motor. these can either be done away with completely by finding a manifold the right length to make up the difference of the now missing restrictor plate or you can simply have the inside diameter milled to match the I.D. of the manifold and put it back in where it was. either way, you still have to contend with the undersized valves. you see where this is headed? it is an entire chain of events that have to happen to get the EPA motor to breath like it should so it will pick up about 8-10 hp.
hope this helps, most of the info has been picked up from other posts/threads on this forum.