I went the other direction, to a 'D' from an 'E' engine. while my EJ22E ecu ran the new motor OK, I swapped in the correct ECU and haven't had any problems, and my fuel economy went up slightly. So that's what I'd recommend, use the ECU from the 22e so you don't have any lights.

One of the biggest things I noticed going from a 22 to a 25 motor is the TORQUE! Immediate instead of having to floor it to feel some. And the fact that the engine doesn't run out of breath like my old motor did at ~5k rpm. The DOHC ecu raised the redline to 6500 as well which can be entertaining, as my motor pulls hard till then. Something I didn't encounter, but you will, is your transmission is a 4.44FD which will affect your car's acceleration quite a bit with the smaller engine. (in a good or bad way?) My auto had 4.11FD and I kinda wish I would have swapped in the 4.44.

Why did I swap? Because the 22e always leaked fluids (mostly oil) and finally blew its headgaskets. I get about 340-350 miles per tank with the 25d, and used to get about 380-400 with the 22e, both with mostly highway driving but I do get on it a bit since the 'D' is a fun engine (but totally not suited for an auto).