I'm confused. Is the DOHC EJ25 in the car and running? Or are you trying to figure out if you can install it in place of the original engine? Which engine is "running on 2 cylinders at idle or when you go into drive it stumbles on 2 cylinders but cleans up when your [sic] going"?
You're basically trying to put a DOHC engine into a car with a stock SOHC engine. The intake manifolds are similar, but different bolt patterns and runner spacing at the heads, so they're not interchangeable. The ECUs and engine wiring harnesses are different. Apparently almost all the sensor wiring is interchangeable, but the IACs are completely different, and that's the major stumbling block.