So I recently replaced the ecu in my 99 gs, and when I put the key in and turn it to the on position without cranking I get a check light and fuel pump primes for about a second and then the dash lights cut out and the tach starts to float. I have a numbers matching ecu, and I've checked all connections and grounds. My question is do I have to get the ecu flashed to my vin #??

Negative. The ECUs aren't that smart in these cars. As long as it is from the same year out of an Eclipse, it should work.

Why did you swap ECUs to start?

The wiring harness had multiple serious breaks which shorted the previous ecu. So I replaced the majority of the harness including the fuse panel, but I did not replace the segment that connects the the ecu after finding no visible damage. I should note that the harness came out of a 97. I tried a 97 ecu and I get signal from the computer and it runs on two cylinders. Which makes sense seeing as the coil pack pin out is different on the 99 compared to the 97. But I am still lost as to why the 99 ecu works but only for a couple of seconds before cutting out?

You need a new harness. The pinouts change almost every single year for the harness. I think 98/99 harnesses are the same. 97 is definitely different.

Originally posted by freelancefool
You need a new harness. The pinouts change almost every single year for the harness. I think 98/99 harnesses are the same. 97 is definitely different.

I understand they are different, and I'd like to know how they are, I have the dealership wiring schematics for the 99 wiring, and I have the Chilton for the other years, and all it says is that the 97 and 99 harnesses have 1 pin out difference as far as the pcm connection goes. (Ie coil pack) but as far as where the pcm harness connects to the engine harness and where the engine harness connects under the dash I would like to see if the pin location is different. (Trying to not have to buy another harness)

Not sure this helps any, but I have 98 block in my 96. Only thing I had to change was the harness for the cps.
So with that in mind, I would think that it's all interchangeable? I mean I've switched several other harnesses and I'm pretty sure I even got the cps harness from a dodge neon..