It can be a big ball of wax depending on exactly what you hope to do. There are minor differences in the onboard hardware between the trims and years that will lead to CEL's but if you're going turbo you're going to have them regardless.
A forum community dedicated to Mitsubishi Eclipse 3G owners and enthusiasts. The immobilizer is deleted so you can swap an 01+ ECU with this ROM into an 00 no problem. Ill be tuning my car with an EVO ecu, but it will be swapped in instead of running dual since Im going manual transmission anyway. There exists an expanded, universal (manual only) ROM that has the definition file necessary to tune big air flows. If big horsepower is your idea then doing an 01+ manual ECU is better. That said, they're only good for naturally aspirated builds as the available XML's do not offer coverage for a few setpoints that need to be changed in order to handle the larger airflow readings that come with turbo setups doing 400+ hp. They have super robust, basic program and cooperate wonderfully compared to some of the older stuff that has more junk in it. I personally prefer tuning 00 cars, federal spec cars especially. Once you have an XML for your ROM you will be able to open it in ECUFlash and make changes to the tune. Many exist, but not all and there is no central source for this information. To do that you need a definition file specifically for your ROM. You can have the tune, but not be able to see it in ECUFlash.
Pulling the read only memory is only half the battle though. Once the Tactrix 2.0 came out that changed because it has an on board PCB that can generate the necessary input sequence and allows you to access the tune. Civic, Mazda RX - 7, Mitsubishi Eclipse and Lancer EVO, Nissan Silvia and Skyline, Subaru Impreza, and Toyota's Altezza, Celica, MR2 Spyder. The older Tactrix 1.3 cables were not capable of outputting that protocol to the ECU and so for a long time they were dubbed "unflashable". The 00 ECU's and a few 01 ECU's use an older processor that requires a different flash protocol (J2354) be used in order to access the read only memory.