Issue with auto to manual conversion

[Buddy]

We have completed the installation of a 6 speed transmission. We are still driving the car with the original auto transmission ECU.
The engine has developed a hesitation. It is intermittent, about every 3 seconds. It's driving me crazy.
I had purchased to install the 2004 ECU that I bought with the transmission, but the auto wiring harness is not compatible with the 6 speed ECU.
Can anyone offer any advice?

Thanks in advance for all of your support.

 

[Honcho]

We have completed the installation of a 6 speed transmission. We are still driving the car with the original auto transmission ECU.
The engine has developed a hesitation. It is intermittent, about every 3 seconds. It's driving me crazy.
I had purchased to install the 2004 ECU that I bought with the transmission, but the auto wiring harness is not compatible with the 6 speed ECU.
Can anyone offer any advice?

Thanks in advance for all of your support.

Hi and congrats on doing the switch. You should not run the 2004 ECU (even if you could) on the 3.0 engine. It is tuned for the MT cams and valve springs and will damage your engine. You should stick with the AT ECU.

There are a lot of potential causes of the hesitation that have nothing to do with the transmission swap. But, there are a few things that could potentially cause it that are swap related. Did you wire the trans neutral and clutch neutral switches? If those are not wired in properly, it will cause the ECU to think the car is either in gear or neutral when you're in motion. Same deal for the "drive" signal. You need to re-wire that switch because, again, it will cause the ECU to think the car is in "drive" when it may not be.

Where did you get the information to do the swap? It's a lot more than just hooking up the AT cables to the ECU.