Honestly...I really didn't agree that your current ECU wouldn't work because it was an auto car. What type of ECU is it? E38/E67 etc?
Did you pin the socket on the harness?
I could be off base here, but an E67 is an E67....For example I have a E67 for a LS3. I have it running an LS7. Additionally, the GM harness didn't have a wire or a pin for the reverse lock-out and I added it and it works fine.
What do you mean by pin the socket on the harness?